BenchmarkSVM_plus_preprocessing_datasets (1).ipynb

{
  "cells": [
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "ux8Di_zAUKj6",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "88463119-0878-4674-a368-954d405cd3b1"
      },
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "1.2.2\n",
            "1.22.4\n",
            "1.5.3\n"
          ]
        }
      ],
      "source": [
        "import pandas\n",
        "import random\n",
        "import numpy as np\n",
        "import sklearn\n",
        "from sklearn.model_selection import GridSearchCV, train_test_split,cross_val_score,StratifiedKFold,KFold\n",
        "from sklearn.metrics import confusion_matrix,accuracy_score,silhouette_score#,calinski_harabaz_score\n",
        "from sklearn.ensemble import GradientBoostingClassifier\n",
        "from sklearn.feature_selection import SelectKBest,f_classif,SelectFdr,RFECV, VarianceThreshold\n",
        "print(sklearn.__version__)\n",
        "print(np.__version__)\n",
        "print(pandas.__version__)\n",
        "from sklearn import svm\n",
        "from sklearn.linear_model import LogisticRegression\n",
        "from sklearn import preprocessing\n",
        "from matplotlib import pyplot as plt\n",
        "from sklearn.preprocessing import normalize,RobustScaler,StandardScaler,MinMaxScaler\n",
        "from mlxtend.evaluate import paired_ttest_5x2cv"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "7e0P7xgqUUMh"
      },
      "outputs": [],
      "source": [
        "# read training data\n",
        "methy = pandas.read_csv(\"methylation2.csv\")\n",
        "mrna = pandas.read_csv(\"mrna.csv\")\n",
        "mirna = pandas.read_csv(\"mirna.csv\")\n",
        "clinical_new = pandas.read_csv(\"clinical_data3.csv\")\n",
        "\n",
        "# CHANGED get the gold class labels directly from the clinical data\n",
        "label_all = clinical_new['class']\n",
        "\n",
        "clinical_new = clinical_new.drop(['Unnamed: 0'], axis = 1)\n",
        "clinical_new = clinical_new[['bcr_patient_barcode','vital_status','survival']]\n",
        "\n",
        "methy = methy.drop(['Unnamed: 0'], axis=1)\n",
        "mrna = mrna.drop(['Unnamed: 0'], axis=1)\n",
        "mirna = mirna.drop(['Unnamed: 0'], axis=1)\n",
        "\n",
        "methy = methy.set_index(['Group.1'])\n",
        "mrna = mrna.set_index(['Group.1'])\n",
        "mirna = mirna.set_index(['GeneSymbol'])\n",
        "\n",
        "methy = methy.transpose()\n",
        "mrna = mrna.transpose()\n",
        "mirna = mirna.transpose()\n",
        "\n",
        "# data log2 transformation\n",
        "mrna = np.log2(mrna+1)\n",
        "mirna = np.log2(mirna+1)"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "SyReh57vUW9t"
      },
      "outputs": [],
      "source": [
        "# vital status has to be 0/1 not 1/2\n",
        "clinical_new[[\"vital_status\"]] = clinical_new[[\"vital_status\"]] -1\n",
        "\n",
        "data_all = pandas.concat([methy,mrna,mirna],axis = 1)\n",
        "data_all2 = data_all.loc[clinical_new['bcr_patient_barcode'],:]"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "6NW3BkfBUcGW"
      },
      "outputs": [],
      "source": [
        "# MODEL-P read in of predictor data\n",
        "#label_all = pandas.read_csv(\"pancreatic cancer/class_label.txt\")\n",
        "#predictor_mrna = pandas.read_csv(\"pancreatic cancer/predictor_mrna.txt\")\n",
        "#predictor_mirna = pandas.read_csv(\"pancreatic cancer/predictor_mirna.txt\")\n",
        "#predictor_methy = pandas.read_csv(\"pancreatic cancer/predictor_methy.txt\")\n",
        "\n",
        "# CHANGED to read in the predictors as csv file, resulting from the single_omics function\n",
        "predictor_mrna = pandas.read_csv(\"mrna_predictors.csv\")\n",
        "predictor_mirna = pandas.read_csv(\"mirna_predictors.csv\")\n",
        "predictor_methy = pandas.read_csv(\"methy_predictors.csv\")"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "axw9PQ2RUnZT"
      },
      "outputs": [],
      "source": [
        "mrna_train = mrna.loc[clinical_new['bcr_patient_barcode'],:]\n",
        "mirna_train = mirna.loc[clinical_new['bcr_patient_barcode'],:]\n",
        "methy_train = methy.loc[clinical_new['bcr_patient_barcode'],:]"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "qFNG9bfSUn4_"
      },
      "outputs": [],
      "source": [
        "# train the classifier for prediction\n",
        "def train_svm(train,test):\n",
        "    #normalizr\n",
        "    train1 = MinMaxScaler().fit_transform(train.transpose()).transpose()\n",
        "    test1 = MinMaxScaler().fit_transform(test.transpose()).transpose()\n",
        "\n",
        "    train1 = RobustScaler().fit_transform(train1)\n",
        "    test1 = RobustScaler().fit_transform(test1)\n",
        "\n",
        "    train1 = pandas.DataFrame(train1,columns = train.columns)\n",
        "    test1 = pandas.DataFrame(test1,columns = test.columns)\n",
        "\n",
        "    # selectfdr feature selection\n",
        "    train_index = SelectFdr(f_classif).fit(train1,label_all).get_support(indices = True)\n",
        "    print(len(train_index))\n",
        "\n",
        "    # CHANGED tests to get variance threshold to use in the Galaxy workflow\n",
        "    # cv_list = []\n",
        "    # for i in range(0, 10):\n",
        "    #   i = i * 0.1\n",
        "    #   train_select = VarianceThreshold(i)\n",
        "    #   train_index = train_select.fit(train1).get_support(indices = True)\n",
        "    #   print(len(train_index))\n",
        "    #   train2 = train1.iloc[:,train_index]\n",
        "    #   test2 = test1.iloc[:,train_index]\n",
        "\n",
        "    #   svm_parameters = {\n",
        "    #   #'kernel': ['rbf','sigmoid','poly','linear'],#\n",
        "    #   'C': [0.0001,0.0005,0.001,0.005,0.01,0.05,0.1,0.5],#,1,1.5,2,2.5,3,3.5,4,4.5,,5.5,6,6.5,7,7.5,8,8.5,9,9.5,10\n",
        "    #   #'coef0': [0.25],\n",
        "    #   'coef0': [0.001,0.005,0.05,0.1,0.25,0.5,0.75,1],#,1.5,2,2.5\n",
        "    #   #'degree' : [2,4,3],\n",
        "    #   'gamma': [0.001,0.005,0.01,0.05,0.1,0.5,1,1.5,2,2.5,3]}#0.0001,0.0005,\n",
        "\n",
        "    #   svm_tune = GridSearchCV(estimator=svm.SVC(kernel = 'sigmoid'),param_grid=svm_parameters,cv=3)\n",
        "    #   svm_tune.fit(train2, label_all)\n",
        "    #   cv_scores = cross_val_score(svm_tune, train2,label_all, cv=5)\n",
        "    #   cvscore_mean = np.mean(cv_scores)\n",
        "    #   print(i, cvscore_mean)\n",
        "    # END tests for variance threshold\n",
        "\n",
        "    # CHANGED tests for RFECV feature selection\n",
        "    #selector = RFECV(estimator=svm.SVC(kernel = 'linear'), min_features_to_select=10, step=1)\n",
        "    #selector = selector.fit(train1, label_all)\n",
        "    #train_index = selector.get_support(indices = True)\n",
        "    #print(len(train_index))\n",
        "    # END tests for RFECV feature selection\n",
        "\n",
        "    train2 = train1.iloc[:,train_index]\n",
        "    test2 = test1.iloc[:,train_index]\n",
        "\n",
        "\n",
        "    svm_parameters = {\n",
        "      #     #'kernel': ['rbf','sigmoid','poly','linear'],#\n",
        "           'C': [0.0001,0.0005,0.001,0.005,0.01,0.05,0.1,0.5],#,1,1.5,2,2.5,3,3.5,4,4.5,,5.5,6,6.5,7,7.5,8,8.5,9,9.5,10\n",
        "      #     #'coef0': [0.25],\n",
        "           'coef0': [0.001,0.005,0.05,0.1,0.25,0.5,0.75,1],#,1.5,2,2.5\n",
        "      #     #'degree' : [2,4,3],\n",
        "           'gamma': [0.001,0.005,0.01,0.05,0.1,0.5,1,1.5,2,2.5,3]}#0.0001,0.0005,\n",
        "\n",
        "    svm_tune = GridSearchCV(estimator=svm.SVC(kernel = 'sigmoid'),param_grid=svm_parameters,cv=3)\n",
        "    svm_tune.fit(train2, label_all)\n",
        "\n",
        "    print(cross_val_score(svm_tune, train2,label_all, cv=3))\n",
        "    print(svm_tune.best_params_)\n",
        "\n",
        "    # predict\n",
        "    pre = svm_tune.predict(test2)\n",
        "    #pre2 = svm_tune.predict_proba(test2)\n",
        "\n",
        "    return pre, train2, test2"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "7ivy4kOMHJGC"
      },
      "source": [
        "## rna seq ICGC"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "GfQrayqlUye7",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "b6c2ec9a-336e-4467-eb65-ab0468703164"
      },
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "109\n"
          ]
        }
      ],
      "source": [
        "# read in the processed test set\n",
        "au_rna = pandas.read_csv(\"rnaseq.tsv\")\n",
        "au_rna = au_rna.set_index(['Unnamed: 0'])\n",
        "\n",
        "# CHANGED because predictor_mrna was in csv format instead of txt\n",
        "common_gene = list(set(predictor_mrna['Group.1']).intersection(set(au_rna.columns)))\n",
        "print(len(common_gene))\n",
        "train_panel = mrna_train[common_gene]\n",
        "test_panel = au_rna[list(common_gene)]\n",
        "\n",
        "# save train and test panel for input in the Galaxy workflows\n",
        "#train_panel.to_csv(\"mrna_trainpanel.csv\", index=False)\n",
        "#test_panel.to_csv(\"mrna_testpanel.csv\", index=False)"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "pred1, train, test = train_svm(train_panel,test_panel)"
      ],
      "metadata": {
        "id": "nzu-g96DaiPg",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "2c17de56-eb71-4c59-d740-720244812054"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "107\n",
            "[0.81632653 0.89795918 0.79166667]\n",
            "{'C': 0.5, 'coef0': 0.25, 'gamma': 0.005}\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "# save predictions in csv for input in Galaxy\n",
        "print(pred1) # made with setting the SVM to SVC(C=0.5, coef0=0.75, gamma=0.01)\n",
        "#pred1.to_csv('mrna_pred_MODELP.csv', index = False)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "fDp85VOCRBnM",
        "outputId": "1e523c88-c792-4cd0-ad47-a5b354c4609a"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "[0 0 0 1 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1\n",
            " 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0 0 0 0 1]\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "# run for variance threshold\n",
        "pred1, train, test = train_svm(train_panel,test_panel)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "fLlvWw0DiqoV",
        "outputId": "43728a2d-ea87-4f28-a2de-1a7d54051fb4"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "109\n",
            "0.0 0.8558620689655172\n",
            "109\n",
            "0.1 0.8558620689655172\n",
            "109\n",
            "0.2 0.8558620689655172\n",
            "109\n",
            "0.30000000000000004 0.8558620689655172\n",
            "104\n",
            "0.4 0.8558620689655172\n",
            "84\n",
            "0.5 0.8282758620689655\n",
            "39\n",
            "0.6000000000000001 0.8216091954022989\n",
            "22\n",
            "0.7000000000000001 0.7593103448275862\n",
            "7\n",
            "0.8 0.8006896551724138\n",
            "2\n",
            "0.9 0.6439080459770116\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "Extra code needed for gathering data for Kaplan-Meier plots"
      ],
      "metadata": {
        "id": "UGgdZ3L6XsQn"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "# filter out the donor_survival_time , donor_vital_status, icgc_donor_id\n",
        "au_rna_cli = pandas.read_csv(\"rnaseq_cli1 (1).tsv\")\n",
        "au_rna_cli_logrank = au_rna_cli[['icgc_donor_id', 'donor_vital_status', 'donor_survival_time']]\n",
        "au_rna_cli_logrank"
      ],
      "metadata": {
        "id": "P_pxpC5pQuEh"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "print(au_rna_cli['icgc_donor_id'].tolist())\n",
        "print(len(au_rna_cli['icgc_donor_id'].tolist()))\n",
        "\n",
        "if au_rna_cli['icgc_donor_id'].tolist() == test_panel.index.tolist():\n",
        "    print(\"The lists are the same.\")\n",
        "else:\n",
        "    print(\"The lists are different.\")"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "uxTwbG3dE6w4",
        "outputId": "15ef8174-a15e-4e63-e9f7-0df1de5c93b2"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "['DO49193', 'DO49178', 'DO49185', 'DO49183', 'DO49168', 'DO49166', 'DO49170', 'DO49164', 'DO49138', 'DO49135', 'DO49133', 'DO49129', 'DO49127', 'DO49130', 'DO49113', 'DO49090', 'DO49079', 'DO49078', 'DO34504', 'DO33168', 'DO33128', 'DO34432', 'DO33472', 'DO33480', 'DO34785', 'DO34793', 'DO34720', 'DO33408', 'DO34736', 'DO33400', 'DO33392', 'DO33376', 'DO34680', 'DO34696', 'DO33336', 'DO33344', 'DO34640', 'DO34656', 'DO34608', 'DO34600', 'DO34336', 'DO34312', 'DO34264', 'DO34240', 'DO34288', 'DO33984', 'DO32900', 'DO32860', 'DO32863', 'DO32875', 'DO32878', 'DO32829', 'DO33600', 'DO34905', 'DO34801', 'DO34817', 'DO33544', 'DO34849', 'DO33512']\n",
            "59\n",
            "The lists are the same.\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "# save new dataframe for further use\n",
        "au_rna_cli_logrank.to_csv('rna_cli_logrank.csv', index=False)"
      ],
      "metadata": {
        "id": "k4_DbR9uYmoH"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "T15gfLU4HBIR"
      },
      "source": [
        "## mrna array ICGC"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "t6i1Wl5sHAIR"
      },
      "outputs": [],
      "source": [
        "au_mrna_array = pandas.read_csv(\"mrna_array.tsv\")\n",
        "\n",
        "au_mrna_array = au_mrna_array.drop(['Unnamed: 0'],axis = 1)\n",
        "au_mrna_array = au_mrna_array.set_index([\"Group.1\"])\n",
        "au_mrna_array = au_mrna_array.transpose()"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "b-yF1MipHXJ4",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "064ea2e2-f547-45d8-9ede-b9ce011424a9"
      },
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "101\n"
          ]
        }
      ],
      "source": [
        "# CHANGED because predictor_mrna was in csv format instead of txt\n",
        "common_gene = set(predictor_mrna['Group.1']).intersection(set(au_mrna_array.columns))\n",
        "print(len(common_gene))\n",
        "train_panel = mrna_train[list(common_gene)]\n",
        "test_panel = au_mrna_array[list(common_gene)]\n"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "# save train and test panel for input in the Galaxy workflows\n",
        "train_panel.to_csv('final_mrna_array_trainpanel.csv', index=False)\n",
        "test_panel.to_csv('final_mrna_array_testpanel.csv', index=False)"
      ],
      "metadata": {
        "id": "A0ew772wv3Ca"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "pred2, train2, test2 = train_svm(train_panel,test_panel)"
      ],
      "metadata": {
        "id": "29txtyxkv_F8",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "d13e253b-9be0-4986-b21c-4d2e1dcb004f"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "99\n",
            "[0.85714286 0.91836735 0.8125    ]\n",
            "{'C': 0.5, 'coef0': 0.001, 'gamma': 0.01}\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "v-56CnmfT6Cy",
        "outputId": "869b8da5-f42d-48b2-d6e7-4b04ffe8b1e5"
      },
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "[0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0\n",
            " 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0]\n"
          ]
        }
      ],
      "source": [
        "print(pred2)\n",
        "\n",
        "pred2 = pandas.DataFrame(pred2)\n",
        "pred2.to_csv('mrna_array_pred_MODELP.csv', index=False)"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "pred2, train2, test2 = train_svm(train_panel,test_panel) # variance threshold run"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "qsedTCP23TdC",
        "outputId": "5cc8e834-2ecf-423d-faaa-1f30acf90621"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "101\n",
            "0.0 0.8558620689655172\n",
            "101\n",
            "0.1 0.8558620689655172\n",
            "101\n",
            "0.2 0.8558620689655172\n",
            "101\n",
            "0.30000000000000004 0.8558620689655172\n",
            "95\n",
            "0.4 0.862758620689655\n",
            "68\n",
            "0.5 0.862758620689655\n",
            "22\n",
            "0.6000000000000001 0.7880459770114943\n",
            "6\n",
            "0.7000000000000001 0.7055172413793104\n",
            "3\n",
            "0.8 0.7055172413793104\n",
            "1\n",
            "0.9 0.7055172413793104\n",
            "1\n",
            "1.0 0.7055172413793104\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "Extra code needed for gathering data for Kaplan-Meier plots"
      ],
      "metadata": {
        "id": "v-VqVUjofUJO"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "mrna_array_cli = pandas.read_csv(\"mrnaarray_cli.tsv\")\n",
        "logrank_mrna_array = mrna_array_cli[['icgc_donor_id', 'donor_vital_status', 'donor_survival_time']]\n",
        "\n",
        "# merge the two DataFrames based on the 'id' column\n",
        "id_df = pandas.DataFrame(test_panel.index, columns=['icgc_donor_id'])\n",
        "merged_id_df = pandas.merge(id_df, logrank_mrna_array, on='icgc_donor_id')\n",
        "\n",
        "if merged_id_df['icgc_donor_id'].tolist() == test_panel.index.tolist():\n",
        "    print(\"The lists are the same.\")\n",
        "else:\n",
        "    print(\"The lists are different.\")\n",
        "\n",
        "#merged_id_df.to_csv('mrna_array_cli_logrank.csv', index=False)"
      ],
      "metadata": {
        "id": "1d1mYmClbnSQ",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "1514a8dd-b0ee-4069-adb3-56c299409fdf"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "The lists are the same.\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "kyM8frxAHgr0"
      },
      "source": [
        "##ICGC methylation"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "bj9sNGlBHNe7"
      },
      "outputs": [],
      "source": [
        "au_methy = pandas.read_csv(\"methylation.tsv\")\n",
        "\n",
        "au_methy = au_methy.drop(['Unnamed: 0'], axis=1)\n",
        "au_methy = au_methy.set_index(['Group.1'])\n",
        "au_methy = au_methy.transpose()"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "id": "bim4M14rHk3G",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "363af72b-b3e0-4a3a-92c2-15b0e5b60476"
      },
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "85\n"
          ]
        }
      ],
      "source": [
        "# CHANGED because predictor_methy was in csv format instead of txt\n",
        "common_gene = set(predictor_methy['Group.1']).intersection(set(au_methy.columns))\n",
        "print(len(common_gene))\n",
        "train_panel = methy_train[list(common_gene)]\n",
        "test_panel = au_methy[list(common_gene)]"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "train_panel.to_csv('final_methy_trainpanel.csv', index=False)\n",
        "test_panel.to_csv('final_methy_testpanel.csv', index=False)"
      ],
      "metadata": {
        "id": "96qCpml1wHu8"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "pred3, train3, test3 = train_svm(train_panel, test_panel)"
      ],
      "metadata": {
        "id": "mY6UCI_lwT6F",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "0dfc2eaa-c350-4fb7-a03d-e04faee376bc"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "81\n",
            "[0.83673469 0.87755102 0.875     ]\n",
            "{'C': 0.5, 'coef0': 0.001, 'gamma': 0.01}\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "print(pred3)\n",
        "pred3 = pandas.DataFrame(pred3)\n",
        "pred3.to_csv('methylation_pred_MODELP.csv', index=False)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "289iq3upWfBp",
        "outputId": "45f33bd4-4dd2-4cb1-dd28-38b9e6a9e803"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "[0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0\n",
            " 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1]\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "pred3, train3, test3 = train_svm(train_panel, test_panel) # variance threshold run"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "IIIOUSvz4qO4",
        "outputId": "42b511af-1635-4c9e-c3d6-265db2ae9aed"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "85\n",
            "0.0 0.8629885057471263\n",
            "84\n",
            "0.1 0.8629885057471263\n",
            "84\n",
            "0.2 0.8629885057471263\n",
            "84\n",
            "0.30000000000000004 0.8629885057471263\n",
            "68\n",
            "0.4 0.8698850574712644\n",
            "24\n",
            "0.5 0.7804597701149426\n",
            "16\n",
            "0.6000000000000001 0.7328735632183908\n",
            "8\n",
            "0.7000000000000001 0.7124137931034482\n",
            "2\n",
            "0.8 0.7055172413793104\n",
            "1\n",
            "0.9 0.7055172413793104\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "Extra code needed for gathering data for Kaplan-Meier plots"
      ],
      "metadata": {
        "id": "xX6ZgT22gRgK"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "methy_cli = pandas.read_csv(\"methy_clinic.tsv\")\n",
        "logrank_methy = methy_cli[['icgc_donor_id.x', 'donor_vital_status', 'donor_survival_time']]\n",
        "\n",
        "# Merge the two DataFrames based on the 'id' column\n",
        "id_df = pandas.DataFrame(test_panel.index, columns=['icgc_donor_id.x'])\n",
        "\n",
        "merged_id_df = pandas.merge(id_df, logrank_methy, on='icgc_donor_id.x')\n",
        "merged_id_df = merged_id_df.drop_duplicates(subset=['icgc_donor_id.x'])\n",
        "\n",
        "if merged_id_df['icgc_donor_id.x'].tolist() == test_panel.index.tolist():\n",
        "    print(\"The lists are the same.\")\n",
        "else:\n",
        "    print(\"The lists are different.\")\n",
        "\n",
        "merged_id_df.to_csv('methy_cli_logrank.csv', index=False)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "j8XL07ZHQNiR",
        "outputId": "26eef49a-9f1c-4fb2-8526-f0c8fd3985a7"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "The lists are the same.\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "## Nanostring experiment geo pdac mirna"
      ],
      "metadata": {
        "id": "6DqR8AqXLLcS"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "geo_mirna = pandas.read_csv(\"mirna.tsv\",sep = \"\\t\")\n",
        "geo_mirna = geo_mirna.set_index(['Unnamed: 0'])\n",
        "\n",
        "# geo_mirna = geo_mirna.drop(['Unnamed: 0'],axis = 1)\n",
        "geo_mirna = np.log2(geo_mirna+1)"
      ],
      "metadata": {
        "id": "KJtYTrMkLRst"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "# CHANGED because predictor_mirna was in csv format instead of txt\n",
        "common_gene = set(predictor_mirna['GeneSymbol']).intersection(set(geo_mirna.columns))\n",
        "train_panel = mirna_train[list(common_gene)]\n",
        "test_panel = geo_mirna[list(common_gene)]"
      ],
      "metadata": {
        "id": "rghyCpK9LkFm"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "# save train and test panel for input in the Galaxy workflows\n",
        "train_panel.to_csv('final_nanostring_trainpanel.csv', index=False)\n",
        "test_panel.to_csv('final_nanostring_testpanel.csv', index=False)"
      ],
      "metadata": {
        "id": "P4r7EBYSLq6j"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "Extra code needed for gathering data for Kaplan-Meier plots"
      ],
      "metadata": {
        "id": "pPIn_oJvuvx3"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "nano_cli = pandas.read_csv(\"geomirna_cli (1).tsv\")\n",
        "logrank_nano = nano_cli[['V1', 'vital_status', 'time']]\n",
        "\n",
        "id_df = pandas.DataFrame(test_panel.index.tolist(), columns=['V1'])\n",
        "\n",
        "# merge the two DataFrames based on the 'id' column\n",
        "merged_id_df = pandas.merge(id_df, logrank_nano, on='V1')\n",
        "\n",
        "if merged_id_df['V1'].tolist() == test_panel.index.tolist():\n",
        "    print(\"The lists are the same.\")\n",
        "else:\n",
        "    print(\"The lists are different.\")\n",
        "\n",
        "merged_id_df.to_csv('nano_cli_logrank.csv', index=False)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "dTfnCEMLgKLo",
        "outputId": "b3e8f60d-bc25-459b-8092-cbdcffe77f91"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "The lists are the same.\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "## COMPASS dataset preparation"
      ],
      "metadata": {
        "id": "oFF8NLj5-zNy"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "clinical_data = pandas.read_csv('Clinical_compass.csv')\n",
        "compass_full_dataset = pandas.read_csv('tpmRSEMCOMPASS.csv')"
      ],
      "metadata": {
        "id": "Fl5K0nH_-3S6"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "# remove patients where treatment response was not examined\n",
        "df = clinical_data.drop(clinical_data[clinical_data['Best response 1st line'] == 'NE'].index)"
      ],
      "metadata": {
        "id": "S_Kg5lZDAinc"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "# create a new column 'response_label' with the same values as 'Best response 1st line'\n",
        "df['response_label'] = df['Best response 1st line']\n",
        "\n",
        "\n",
        "# change the labels from PR and SD to 0 and PD to 1\n",
        "# 0 refers to response to treatment, 1 refers to non_respons to treatment\n",
        "df.loc[df['Best response 1st line'] == 'PR', 'response_label'] = 0\n",
        "df.loc[df['Best response 1st line'] == 'SD', 'response_label'] = 0\n",
        "df.loc[df['Best response 1st line'] == 'PD', 'response_label'] = 1"
      ],
      "metadata": {
        "id": "eH58B6YEAuA4"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "# keep only patient ID (PCSI ID) and response label\n",
        "selected_columns = ['PCSI ID', 'response_label']\n",
        "response_df = df.loc[:, selected_columns]"
      ],
      "metadata": {
        "id": "X3p8ZhNJC5fp"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "Preprocess the full dataset with gene information"
      ],
      "metadata": {
        "id": "egxikbpzwaFq"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "compass_full_dataset.head(10)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 473
        },
        "id": "QPk7Rqgj_nyg",
        "outputId": "369f52ae-6f9c-4913-f44c-2c6cf02e2f96"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "  Unnamed: 0  PCSI_1001  PCSI_1003  PCSI_1004  PCSI_1005  PCSI_1007  \\\n",
              "0       A1BG       0.00       0.00       0.00       0.00       0.00   \n",
              "1       A1CF       0.63       0.00       0.00       0.00       0.00   \n",
              "2        A2M       9.58       2.67       4.28       1.75       5.82   \n",
              "3      A2ML1       0.00       1.06       0.00       3.00       0.00   \n",
              "4     A4GALT       3.28       0.00       3.45       2.10       0.00   \n",
              "5      A4GNT       0.00       0.00       0.00       0.00       0.00   \n",
              "6       AAAS       3.92      12.92       2.22       5.39       2.77   \n",
              "7       AACS       2.09       0.00       1.09       1.34       0.00   \n",
              "8      AADAC      19.08       0.00       0.00       0.00       0.00   \n",
              "9      AADAT       0.00       0.00       0.00       0.00       0.00   \n",
              "\n",
              "   PCSI_1008  PCSI_1009  PCSI_1010  PCSI_1011  ...  PCSI_0986  PCSI_0987  \\\n",
              "0       1.74       0.00       0.00       0.00  ...       0.00       0.00   \n",
              "1       0.00       0.71       0.00       0.00  ...       0.81       1.62   \n",
              "2       0.00      10.18       1.56       0.00  ...       1.76       0.00   \n",
              "3       0.00       0.00       0.00       0.00  ...       0.00       0.00   \n",
              "4       0.00       0.00       0.00       0.00  ...       0.00       0.00   \n",
              "5       0.00       0.00       0.00       0.00  ...       0.00       0.00   \n",
              "6       7.34       8.80      13.65       4.37  ...       5.40       3.70   \n",
              "7       0.00       2.28       0.00       0.00  ...       0.00       0.00   \n",
              "8       0.00       0.00       0.00       4.97  ...       0.00       0.00   \n",
              "9       0.00       0.00       0.00       0.00  ...       0.00       0.00   \n",
              "\n",
              "   PCSI_0989  PCSI_0991  PCSI_0992  PCSI_0993  PCSI_0994  PCSI_0996  \\\n",
              "0       0.00       0.00       0.00       0.00       0.00       0.00   \n",
              "1       0.00       1.03       0.00       0.00       0.00       0.00   \n",
              "2       2.31       4.45      11.25      11.27       2.29       0.00   \n",
              "3       0.00       0.00       0.00       0.00       0.00       0.00   \n",
              "4       0.00       0.00       0.00       0.00       0.00       0.00   \n",
              "5       0.00       0.00       0.00       0.00       0.00       0.00   \n",
              "6       0.00       6.85       0.00      10.49       0.00       5.35   \n",
              "7       0.00       0.00       5.74       0.00       3.49       0.00   \n",
              "8       0.00       0.00       0.00       0.00       0.00       0.00   \n",
              "9       0.00       0.00       0.00       0.00       0.00       2.04   \n",
              "\n",
              "   PCSI_0998  PCSI_0999  \n",
              "0       0.00       0.00  \n",
              "1       0.00       0.00  \n",
              "2       0.00       2.31  \n",
              "3       1.28       0.00  \n",
              "4       0.00       0.00  \n",
              "5       0.00       0.00  \n",
              "6       0.00       2.62  \n",
              "7       0.00       1.28  \n",
              "8       0.00       0.00  \n",
              "9       0.00       0.00  \n",
              "\n",
              "[10 rows x 195 columns]"
            ],
            "text/html": [
              "\n",
              "  <div id=\"df-2a6ab78d-fdef-409d-854b-00af5af0a80e\">\n",
              "    <div class=\"colab-df-container\">\n",
              "      <div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
              "    }\n",
              "\n",
              "    .dataframe tbody tr th {\n",
              "        vertical-align: top;\n",
              "    }\n",
              "\n",
              "    .dataframe thead th {\n",
              "        text-align: right;\n",
              "    }\n",
              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>Unnamed: 0</th>\n",
              "      <th>PCSI_1001</th>\n",
              "      <th>PCSI_1003</th>\n",
              "      <th>PCSI_1004</th>\n",
              "      <th>PCSI_1005</th>\n",
              "      <th>PCSI_1007</th>\n",
              "      <th>PCSI_1008</th>\n",
              "      <th>PCSI_1009</th>\n",
              "      <th>PCSI_1010</th>\n",
              "      <th>PCSI_1011</th>\n",
              "      <th>...</th>\n",
              "      <th>PCSI_0986</th>\n",
              "      <th>PCSI_0987</th>\n",
              "      <th>PCSI_0989</th>\n",
              "      <th>PCSI_0991</th>\n",
              "      <th>PCSI_0992</th>\n",
              "      <th>PCSI_0993</th>\n",
              "      <th>PCSI_0994</th>\n",
              "      <th>PCSI_0996</th>\n",
              "      <th>PCSI_0998</th>\n",
              "      <th>PCSI_0999</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>A1BG</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>1.74</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>...</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>A1CF</td>\n",
              "      <td>0.63</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.71</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>...</td>\n",
              "      <td>0.81</td>\n",
              "      <td>1.62</td>\n",
              "      <td>0.00</td>\n",
              "      <td>1.03</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>A2M</td>\n",
              "      <td>9.58</td>\n",
              "      <td>2.67</td>\n",
              "      <td>4.28</td>\n",
              "      <td>1.75</td>\n",
              "      <td>5.82</td>\n",
              "      <td>0.00</td>\n",
              "      <td>10.18</td>\n",
              "      <td>1.56</td>\n",
              "      <td>0.00</td>\n",
              "      <td>...</td>\n",
              "      <td>1.76</td>\n",
              "      <td>0.00</td>\n",
              "      <td>2.31</td>\n",
              "      <td>4.45</td>\n",
              "      <td>11.25</td>\n",
              "      <td>11.27</td>\n",
              "      <td>2.29</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>2.31</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>A2ML1</td>\n",
              "      <td>0.00</td>\n",
              "      <td>1.06</td>\n",
              "      <td>0.00</td>\n",
              "      <td>3.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>...</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>1.28</td>\n",
              "      <td>0.00</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>A4GALT</td>\n",
              "      <td>3.28</td>\n",
              "      <td>0.00</td>\n",
              "      <td>3.45</td>\n",
              "      <td>2.10</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>...</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5</th>\n",
              "      <td>A4GNT</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>...</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>6</th>\n",
              "      <td>AAAS</td>\n",
              "      <td>3.92</td>\n",
              "      <td>12.92</td>\n",
              "      <td>2.22</td>\n",
              "      <td>5.39</td>\n",
              "      <td>2.77</td>\n",
              "      <td>7.34</td>\n",
              "      <td>8.80</td>\n",
              "      <td>13.65</td>\n",
              "      <td>4.37</td>\n",
              "      <td>...</td>\n",
              "      <td>5.40</td>\n",
              "      <td>3.70</td>\n",
              "      <td>0.00</td>\n",
              "      <td>6.85</td>\n",
              "      <td>0.00</td>\n",
              "      <td>10.49</td>\n",
              "      <td>0.00</td>\n",
              "      <td>5.35</td>\n",
              "      <td>0.00</td>\n",
              "      <td>2.62</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7</th>\n",
              "      <td>AACS</td>\n",
              "      <td>2.09</td>\n",
              "      <td>0.00</td>\n",
              "      <td>1.09</td>\n",
              "      <td>1.34</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>2.28</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>...</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>5.74</td>\n",
              "      <td>0.00</td>\n",
              "      <td>3.49</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>1.28</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>8</th>\n",
              "      <td>AADAC</td>\n",
              "      <td>19.08</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>4.97</td>\n",
              "      <td>...</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>9</th>\n",
              "      <td>AADAT</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>...</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "      <td>2.04</td>\n",
              "      <td>0.00</td>\n",
              "      <td>0.00</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>10 rows × 195 columns</p>\n",
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          },
          "metadata": {},
          "execution_count": 73
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "compass_full_dataset = compass_full_dataset.set_index('Unnamed: 0')"
      ],
      "metadata": {
        "id": "ey7jXGteG0tx"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "# select only the patient columns where we have a treatment response label for\n",
        "common_patient = set(response_df['PCSI ID']).intersection(set(compass_full_dataset.columns))\n",
        "filtered_compass = compass_full_dataset[list(common_patient)]\n"
      ],
      "metadata": {
        "id": "LkSP1sIvEnJj"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "# remove the genes with more than 40% zero values\n",
        "filtered_compass = filtered_compass.transpose()\n",
        "small_filtered_compass = filtered_compass.loc[:, filtered_compass.eq(0).mean() < .40]"
      ],
      "metadata": {
        "id": "GFbje5wMXdMW"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "small_filtered_compass = np.log2(small_filtered_compass +1)"
      ],
      "metadata": {
        "id": "1q-Xf7v3abzL"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "small_filtered_compass"
      ],
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        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 505
        },
        "id": "GC4kXxOiCFZN",
        "outputId": "dd5ce0c4-b4e7-426f-f74b-862f887eb3de"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
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              "Unnamed: 0       A2M      AAAS      AAK1      AAMP     AARS1      AATF  \\\n",
              "PCSI_0714   4.286142  2.792855  2.531069  3.937344  4.428276  3.670161   \n",
              "PCSI_0612   3.001802  2.972693  1.411426  3.549669  2.046142  0.000000   \n",
              "PCSI_0778   2.503349  2.592158  0.000000  0.000000  2.903038  2.313246   \n",
              "PCSI_1056   1.575312  2.851999  4.316870  2.811471  1.867896  2.560715   \n",
              "PCSI_0647   3.257011  3.214125  2.948601  2.754888  3.904966  3.005400   \n",
              "...              ...       ...       ...       ...       ...       ...   \n",
              "PCSI_0719   4.050502  2.801159  2.746313  3.749534  1.891419  0.000000   \n",
              "PCSI_1026   3.990955  3.724650  3.580145  3.779260  3.092546  2.985500   \n",
              "PCSI_0695   1.778209  3.654206  1.438293  2.241840  2.558268  0.000000   \n",
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              "PCSI_1035   0.000000  3.684819  3.782409  2.272023  3.493135  2.859970   \n",
              "\n",
              "Unnamed: 0     ABCA1     ABCA2     ABCB7     ABCC1  ...    ZNF888     ZNF91  \\\n",
              "PCSI_0714   1.117695  2.010780  1.941106  1.827819  ...  2.869871  3.673556   \n",
              "PCSI_0612   0.956057  1.500802  0.000000  0.000000  ...  6.357376  8.650836   \n",
              "PCSI_0778   1.207893  0.000000  1.384050  1.650765  ...  7.286049  1.875780   \n",
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              "PCSI_0647   1.339137  0.584963  0.963474  1.531069  ...  7.831054  8.227857   \n",
              "...              ...       ...       ...       ...  ...       ...       ...   \n",
              "PCSI_0719   1.389567  1.042644  0.000000  2.117695  ...  2.761285  5.169925   \n",
              "PCSI_1026   1.941106  1.310340  1.257011  2.720278  ...  2.073820  5.555509   \n",
              "PCSI_0695   2.292782  1.182692  0.000000  0.000000  ...  5.590063  5.393004   \n",
              "PCSI_0712   1.250962  0.000000  0.887525  1.937344  ...  2.788686  5.666473   \n",
              "PCSI_1035   1.356144  0.000000  0.000000  1.827819  ...  2.935460  3.883621   \n",
              "\n",
              "Unnamed: 0     ZNF92     ZNF93     ZNFX1      ZPR1    ZRANB2    ZSWIM8  \\\n",
              "PCSI_0714   3.240314  2.104337  0.000000  0.704872  2.897240  1.618239   \n",
              "PCSI_0612   5.912410  1.594549  1.910733  0.839960  1.575312  1.427606   \n",
              "PCSI_0778   3.144046  0.000000  0.000000  2.097611  0.000000  1.117695   \n",
              "PCSI_1056   4.435629  0.000000  1.117695  0.739848  1.416840  0.782409   \n",
              "PCSI_0647   7.273236  1.400538  1.704872  0.704872  1.378512  1.238787   \n",
              "...              ...       ...       ...       ...       ...       ...   \n",
              "PCSI_0719   2.090853  1.459432  2.198494  0.000000  2.147307  1.678072   \n",
              "PCSI_1026   4.919817  0.000000  2.587365  0.000000  2.521051  2.330558   \n",
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              "Unnamed: 0       ZYX     ZZEF1  \n",
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              "PCSI_0719   3.344828  0.790772  \n",
              "PCSI_1026   2.931683  0.000000  \n",
              "PCSI_0695   1.963474  0.000000  \n",
              "PCSI_0712   1.545968  1.356144  \n",
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              "      <th>Unnamed: 0</th>\n",
              "      <th>A2M</th>\n",
              "      <th>AAAS</th>\n",
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              "      <th>AAMP</th>\n",
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              "  <tbody>\n",
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              "      <th>PCSI_0714</th>\n",
              "      <td>4.286142</td>\n",
              "      <td>2.792855</td>\n",
              "      <td>2.531069</td>\n",
              "      <td>3.937344</td>\n",
              "      <td>4.428276</td>\n",
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              "      <td>2.010780</td>\n",
              "      <td>1.941106</td>\n",
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              "      <td>1.618239</td>\n",
              "      <td>3.253989</td>\n",
              "      <td>0.765535</td>\n",
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              "      <th>PCSI_0612</th>\n",
              "      <td>3.001802</td>\n",
              "      <td>2.972693</td>\n",
              "      <td>1.411426</td>\n",
              "      <td>3.549669</td>\n",
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              "      <td>8.650836</td>\n",
              "      <td>5.912410</td>\n",
              "      <td>1.594549</td>\n",
              "      <td>1.910733</td>\n",
              "      <td>0.839960</td>\n",
              "      <td>1.575312</td>\n",
              "      <td>1.427606</td>\n",
              "      <td>1.859970</td>\n",
              "      <td>0.000000</td>\n",
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              "      <th>PCSI_0778</th>\n",
              "      <td>2.503349</td>\n",
              "      <td>2.592158</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>2.903038</td>\n",
              "      <td>2.313246</td>\n",
              "      <td>1.207893</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>1.384050</td>\n",
              "      <td>1.650765</td>\n",
              "      <td>...</td>\n",
              "      <td>7.286049</td>\n",
              "      <td>1.875780</td>\n",
              "      <td>3.144046</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>2.097611</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>1.117695</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>0.000000</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>PCSI_1056</th>\n",
              "      <td>1.575312</td>\n",
              "      <td>2.851999</td>\n",
              "      <td>4.316870</td>\n",
              "      <td>2.811471</td>\n",
              "      <td>1.867896</td>\n",
              "      <td>2.560715</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>0.604071</td>\n",
              "      <td>0.992768</td>\n",
              "      <td>1.207893</td>\n",
              "      <td>...</td>\n",
              "      <td>1.090853</td>\n",
              "      <td>6.480265</td>\n",
              "      <td>4.435629</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>1.117695</td>\n",
              "      <td>0.739848</td>\n",
              "      <td>1.416840</td>\n",
              "      <td>0.782409</td>\n",
              "      <td>1.739848</td>\n",
              "      <td>0.000000</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>PCSI_0647</th>\n",
              "      <td>3.257011</td>\n",
              "      <td>3.214125</td>\n",
              "      <td>2.948601</td>\n",
              "      <td>2.754888</td>\n",
              "      <td>3.904966</td>\n",
              "      <td>3.005400</td>\n",
              "      <td>1.339137</td>\n",
              "      <td>0.584963</td>\n",
              "      <td>0.963474</td>\n",
              "      <td>1.531069</td>\n",
              "      <td>...</td>\n",
              "      <td>7.831054</td>\n",
              "      <td>8.227857</td>\n",
              "      <td>7.273236</td>\n",
              "      <td>1.400538</td>\n",
              "      <td>1.704872</td>\n",
              "      <td>0.704872</td>\n",
              "      <td>1.378512</td>\n",
              "      <td>1.238787</td>\n",
              "      <td>2.395063</td>\n",
              "      <td>0.432959</td>\n",
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              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
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              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
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              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
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              "      <th>PCSI_0719</th>\n",
              "      <td>4.050502</td>\n",
              "      <td>2.801159</td>\n",
              "      <td>2.746313</td>\n",
              "      <td>3.749534</td>\n",
              "      <td>1.891419</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>1.389567</td>\n",
              "      <td>1.042644</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>2.117695</td>\n",
              "      <td>...</td>\n",
              "      <td>2.761285</td>\n",
              "      <td>5.169925</td>\n",
              "      <td>2.090853</td>\n",
              "      <td>1.459432</td>\n",
              "      <td>2.198494</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>2.147307</td>\n",
              "      <td>1.678072</td>\n",
              "      <td>3.344828</td>\n",
              "      <td>0.790772</td>\n",
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              "    <tr>\n",
              "      <th>PCSI_1026</th>\n",
              "      <td>3.990955</td>\n",
              "      <td>3.724650</td>\n",
              "      <td>3.580145</td>\n",
              "      <td>3.779260</td>\n",
              "      <td>3.092546</td>\n",
              "      <td>2.985500</td>\n",
              "      <td>1.941106</td>\n",
              "      <td>1.310340</td>\n",
              "      <td>1.257011</td>\n",
              "      <td>2.720278</td>\n",
              "      <td>...</td>\n",
              "      <td>2.073820</td>\n",
              "      <td>5.555509</td>\n",
              "      <td>4.919817</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>2.587365</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>2.521051</td>\n",
              "      <td>2.330558</td>\n",
              "      <td>2.931683</td>\n",
              "      <td>0.000000</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>PCSI_0695</th>\n",
              "      <td>1.778209</td>\n",
              "      <td>3.654206</td>\n",
              "      <td>1.438293</td>\n",
              "      <td>2.241840</td>\n",
              "      <td>2.558268</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>2.292782</td>\n",
              "      <td>1.182692</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>...</td>\n",
              "      <td>5.590063</td>\n",
              "      <td>5.393004</td>\n",
              "      <td>4.723012</td>\n",
              "      <td>3.976364</td>\n",
              "      <td>1.655352</td>\n",
              "      <td>1.790772</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>0.910733</td>\n",
              "      <td>1.963474</td>\n",
              "      <td>0.000000</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>PCSI_0712</th>\n",
              "      <td>3.122673</td>\n",
              "      <td>4.310340</td>\n",
              "      <td>2.939227</td>\n",
              "      <td>1.847997</td>\n",
              "      <td>2.976364</td>\n",
              "      <td>2.877744</td>\n",
              "      <td>1.250962</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>0.887525</td>\n",
              "      <td>1.937344</td>\n",
              "      <td>...</td>\n",
              "      <td>2.788686</td>\n",
              "      <td>5.666473</td>\n",
              "      <td>4.130931</td>\n",
              "      <td>1.321928</td>\n",
              "      <td>2.601697</td>\n",
              "      <td>1.454176</td>\n",
              "      <td>3.040892</td>\n",
              "      <td>2.241840</td>\n",
              "      <td>1.545968</td>\n",
              "      <td>1.356144</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>PCSI_1035</th>\n",
              "      <td>0.000000</td>\n",
              "      <td>3.684819</td>\n",
              "      <td>3.782409</td>\n",
              "      <td>2.272023</td>\n",
              "      <td>3.493135</td>\n",
              "      <td>2.859970</td>\n",
              "      <td>1.356144</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>1.827819</td>\n",
              "      <td>...</td>\n",
              "      <td>2.935460</td>\n",
              "      <td>3.883621</td>\n",
              "      <td>3.488001</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>1.333424</td>\n",
              "      <td>0.903038</td>\n",
              "      <td>2.897240</td>\n",
              "      <td>0.948601</td>\n",
              "      <td>0.000000</td>\n",
              "      <td>0.956057</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>157 rows × 3493 columns</p>\n",
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              "  "
            ]
          },
          "metadata": {},
          "execution_count": 125
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "# the rows correspond with the patients, columns correspond with the genes\n",
        "small_filtered_compass.to_csv('preprocessed_tpmRSEMCOMPASS1.csv', index=False)"
      ],
      "metadata": {
        "id": "vsK7Iue0bBmz"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "Create csv file with gold labels of COMPASS dataset"
      ],
      "metadata": {
        "id": "BfxUSNFzwI5I"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "response_df"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 423
        },
        "id": "JJKMMcz60_Iw",
        "outputId": "49c8254c-c93e-4556-82b9-8503540e9886"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "       PCSI ID response_label\n",
              "0    PCSI_0630              0\n",
              "1    PCSI_0632              0\n",
              "2    PCSI_0634              0\n",
              "3    PCSI_0637              0\n",
              "4    PCSI_0640              0\n",
              "..         ...            ...\n",
              "188  PCSI_1066              0\n",
              "189  PCSI_1068              0\n",
              "190  PCSI_1070              0\n",
              "191  PCSI_1071              0\n",
              "193  PCSI_1093              0\n",
              "\n",
              "[159 rows x 2 columns]"
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              "      <th>PCSI ID</th>\n",
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              "      <th>193</th>\n",
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              "            + ' to learn more about interactive tables.';\n",
              "          element.innerHTML = '';\n",
              "          dataTable['output_type'] = 'display_data';\n",
              "          await google.colab.output.renderOutput(dataTable, element);\n",
              "          const docLink = document.createElement('div');\n",
              "          docLink.innerHTML = docLinkHtml;\n",
              "          element.appendChild(docLink);\n",
              "        }\n",
              "      </script>\n",
              "    </div>\n",
              "  </div>\n",
              "  "
            ]
          },
          "metadata": {},
          "execution_count": 113
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "response_df = response_df.transpose()"
      ],
      "metadata": {
        "id": "t_Pf5aKNMMSu"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "# set patient id as column names\n",
        "response_df.columns = response_df.loc['PCSI ID', :].values"
      ],
      "metadata": {
        "id": "gBRHW7BFMizk"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "response_df = response_df.drop('PCSI ID', axis=0)"
      ],
      "metadata": {
        "id": "yNCK5rizMUyT"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "# select only the patient columns where we have a treatment response label for\n",
        "response_df = response_df[list(common_patient)]"
      ],
      "metadata": {
        "id": "NtP3t0rIMxVZ"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "response_df = response_df.transpose()"
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      "metadata": {
        "id": "99JIfvYSRIVT"
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      "execution_count": null,
      "outputs": []
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      "execution_count": null,
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              "          response_label\n",
              "PCSI_0714              1\n",
              "PCSI_0612              0\n",
              "PCSI_0778              0\n",
              "PCSI_1056              0\n",
              "PCSI_0647              0\n",
              "...                  ...\n",
              "PCSI_0719              0\n",
              "PCSI_1026              1\n",
              "PCSI_0695              0\n",
              "PCSI_0712              0\n",
              "PCSI_1035              0\n",
              "\n",
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              "\n",
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        "response_df = response_df.reset_index(drop=True)\n",
        "response_df"
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        "id": "U5Wqe92RTPSq",
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          "base_uri": "https://localhost:8080/",
          "height": 423
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        "outputId": "a39fd976-b6e6-416b-8754-dc0f698f9652"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "    response_label\n",
              "0                1\n",
              "1                0\n",
              "2                0\n",
              "3                0\n",
              "4                0\n",
              "..             ...\n",
              "152              0\n",
              "153              1\n",
              "154              0\n",
              "155              0\n",
              "156              0\n",
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              "[157 rows x 1 columns]"
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              "      </button>\n",
              "      \n",
              "  <style>\n",
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              "      flex-wrap:wrap;\n",
              "      gap: 12px;\n",
              "    }\n",
              "\n",
              "    .colab-df-convert {\n",
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              "    }\n",
              "\n",
              "    .colab-df-convert:hover {\n",
              "      background-color: #E2EBFA;\n",
              "      box-shadow: 0px 1px 2px rgba(60, 64, 67, 0.3), 0px 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
              "      fill: #174EA6;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert {\n",
              "      background-color: #3B4455;\n",
              "      fill: #D2E3FC;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert:hover {\n",
              "      background-color: #434B5C;\n",
              "      box-shadow: 0px 1px 3px 1px rgba(0, 0, 0, 0.15);\n",
              "      filter: drop-shadow(0px 1px 2px rgba(0, 0, 0, 0.3));\n",
              "      fill: #FFFFFF;\n",
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              "  </style>\n",
              "\n",
              "      <script>\n",
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              "          google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "\n",
              "        async function convertToInteractive(key) {\n",
              "          const element = document.querySelector('#df-35a43267-0407-49e6-9369-f200ac72a08b');\n",
              "          const dataTable =\n",
              "            await google.colab.kernel.invokeFunction('convertToInteractive',\n",
              "                                                     [key], {});\n",
              "          if (!dataTable) return;\n",
              "\n",
              "          const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "            '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
              "            + ' to learn more about interactive tables.';\n",
              "          element.innerHTML = '';\n",
              "          dataTable['output_type'] = 'display_data';\n",
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              "          docLink.innerHTML = docLinkHtml;\n",
              "          element.appendChild(docLink);\n",
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              "  </div>\n",
              "  "
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          "metadata": {},
          "execution_count": 122
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      ]
    },
    {
      "cell_type": "code",
      "source": [
        "response_df = response_df.astype('int')"
      ],
      "metadata": {
        "id": "uyVl4UJYTS3U"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "response_df.to_csv('response_labels.csv', index=False)"
      ],
      "metadata": {
        "id": "txNEz_wayGOH"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "## Iknowit dataset preparation\n"
      ],
      "metadata": {
        "id": "ic4Xgb5Z7EtR"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "full_dataset = pandas.read_excel('processed_Folfirinox_iknowit2.xlsx')"
      ],
      "metadata": {
        "id": "WRIckE_m7Jzg"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "full_dataset"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 1000
        },
        "id": "F-evvqel7Ql5",
        "outputId": "5579dd56-f3e0-4a82-ace4-0220ac5fde50"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "    Unnamed: 0  Sample.ID  Pair      Time             Response     IRF5.  \\\n",
              "0            1  PA-180001     1  Baseline      Disease Control  8.175069   \n",
              "1            2  PA-180013     7  Baseline      Disease Control  7.897230   \n",
              "2            3  PA-180022     9  Baseline      Disease Control  7.959287   \n",
              "3            4  PA-180044    14  Baseline      Disease Control  8.094771   \n",
              "4            5  PA-180062    17  Baseline      Disease Control  7.712696   \n",
              "5            6  PA-180065    19  Baseline      Disease Control  7.985200   \n",
              "6            7  PA-180107    24  Baseline      Disease Control  7.830536   \n",
              "7            8  PA-190147    32  Baseline      Disease Control  7.141266   \n",
              "8            9  PA-190170    34  Baseline      Disease Control  7.937708   \n",
              "9           10  PA-190190    36  Baseline      Disease Control  7.873866   \n",
              "10          11  PA-190223    38  Baseline      Disease Control  8.178088   \n",
              "11          12  PA-190254    43  Baseline      Disease Control  7.459166   \n",
              "12          13  PA-190308    44  Baseline      Disease Control  7.592571   \n",
              "13          14  PA-190313    45  Baseline      Disease Control  7.992748   \n",
              "14          15  PA-190414    46  Baseline      Disease Control  8.589231   \n",
              "15          16  PA-190572    53  Baseline      Disease Control  7.731146   \n",
              "16          17  PA-190680    57  Baseline      Disease Control  8.131546   \n",
              "17          18  PA-200719    58  Baseline      Disease Control  7.489974   \n",
              "18          19  PA-201112    70  Baseline      Disease Control  8.090021   \n",
              "19          20  PA-201145    71  Baseline      Disease Control  8.097897   \n",
              "20          21  PA-201162    72  Baseline      Disease Control  7.690138   \n",
              "21          22  PA-201182    73  Baseline      Disease Control  7.108122   \n",
              "22          23  PA-201237    76  Baseline      Disease Control  8.053538   \n",
              "23          24  PA-201291    77  Baseline      Disease Control  7.596235   \n",
              "24          25  PA-211459    79  Baseline      Disease Control  8.215981   \n",
              "25          26  PA-180030    10  Baseline      Disease Control  8.376898   \n",
              "26          27  PA-180039    12  Baseline      Disease Control  7.730115   \n",
              "27          28  PA-180063    18  Baseline      Disease Control  8.004767   \n",
              "28          29  PA-180072    20  Baseline      Disease Control  7.403809   \n",
              "29          30  PA-180092    23  Baseline      Disease Control  8.127504   \n",
              "30          31  PA-190135    27  Baseline      Disease Control  8.907368   \n",
              "31          32  PA-190136    28  Baseline      Disease Control  7.753025   \n",
              "32          33  PA-190142    31  Baseline      Disease Control  8.191004   \n",
              "33          34  PA-150167    33  Baseline      Disease Control  7.443794   \n",
              "34          35  PA-190172    35  Baseline      Disease Control  7.423817   \n",
              "35          36  PA-190415    47  Baseline      Disease Control  8.244706   \n",
              "36          37  PA-190534    51  Baseline      Disease Control  7.796751   \n",
              "37          38  PA-190625    55  Baseline      Disease Control  8.087970   \n",
              "38          39  PA-200787    60  Baseline      Disease Control  8.374411   \n",
              "39          40  PA-200851    63  Baseline      Disease Control  7.804807   \n",
              "40          41  PA-200997    65  Baseline      Disease Control  7.929206   \n",
              "41          42  PA-201007    66  Baseline      Disease Control  7.323598   \n",
              "42          43  PA-201070    67  Baseline      Disease Control  8.130442   \n",
              "43          44  PA-201079    68  Baseline      Disease Control  8.085347   \n",
              "44          45  PA-201186    74  Baseline      Disease Control  7.823197   \n",
              "45          46  PA-201217    75  Baseline      Disease Control  8.103853   \n",
              "46          47  PA-201357    78  Baseline      Disease Control  7.574504   \n",
              "47          48  PA-211498    80  Baseline      Disease Control  7.965346   \n",
              "48          98  PA-180055    15  Baseline  Progressive Disease  8.442854   \n",
              "49          99  PA-180089    22  Baseline  Progressive Disease  8.045827   \n",
              "50         100  PA-190228    39  Baseline  Progressive Disease  7.668532   \n",
              "51         101  PA-201092    69  Baseline  Progressive Disease  8.196647   \n",
              "52         102  PA-180058    16  Baseline  Progressive Disease  7.970761   \n",
              "53         103  PA-190250    41  Baseline  Progressive Disease  7.635382   \n",
              "54         104  PA-190487    49  Baseline  Progressive Disease  7.721606   \n",
              "55         105  PA-200870    64  Baseline  Progressive Disease  7.626712   \n",
              "\n",
              "       ELK1.    C4BPA.       C7.   CASP10.  ...     ANXA1.  POU2AF1.  \\\n",
              "0   6.351946  4.154007  2.651507  7.304949  ...  13.044361  5.154007   \n",
              "1   6.483671  3.253374  3.012365  6.619023  ...  12.706644  6.970786   \n",
              "2   6.353566  2.315431  2.830004  6.784200  ...  12.859843  6.959287   \n",
              "3   6.567792  7.465912  3.108360  6.705295  ...  13.300776  6.161471   \n",
              "4   5.380679  2.869717  2.717714  6.851570  ...  12.977980  6.262034   \n",
              "5   6.264817  2.550572  2.550572  6.740396  ...  13.239368  5.408553   \n",
              "6   6.147271  1.446831  2.616756  6.685236  ...  12.737570  6.001420   \n",
              "7   0.399799  3.207154  2.984762  6.859231  ...  13.556515  6.422167   \n",
              "8   6.604973  3.134653  2.549690  6.825815  ...  13.564844  5.889540   \n",
              "9   5.431644  3.367513  2.230010  6.580507  ...  13.009729  5.580507   \n",
              "10  6.842104  7.618871  2.489588  6.748322  ...  13.212152  6.074551   \n",
              "11  6.213801  3.985995  2.323030  6.410493  ...  12.936666  5.966886   \n",
              "12  6.558083  8.087702  2.411241  6.233243  ...  12.954549  5.581166   \n",
              "13  6.440575  3.964842  3.134767  6.692762  ...  13.184767  5.665282   \n",
              "14  5.184247  6.236714  2.751287  7.558642  ...  13.439538  5.638813   \n",
              "15  6.414289  3.829327  2.751324  6.658215  ...  12.865645  5.388754   \n",
              "16  6.857624  3.398192  3.398192  6.983154  ...  13.237711  6.720120   \n",
              "17  6.284860  3.574367  2.114935  6.829180  ...  12.832611  5.507252   \n",
              "18  6.476769  4.573445  2.988483  6.403520  ...  13.223699  6.462414   \n",
              "19  6.441967  2.547150  3.354505  6.441967  ...  12.975379  6.392640   \n",
              "20  6.472782  3.530267  2.530267  6.363157  ...  12.915860  5.922584   \n",
              "21  6.059213  4.956119  3.371157  6.288694  ...  13.098699  5.660663   \n",
              "22  4.333926  5.454220  1.810364  6.918888  ...  13.838011  5.960111   \n",
              "23  6.654338  4.264391  3.313301  6.106850  ...  13.109449  6.276775   \n",
              "24  5.806590  2.543555  3.681059  6.760786  ...  13.220570  5.745189   \n",
              "25  6.812113  3.364654  2.227150  7.085131  ...  12.676299  6.646689   \n",
              "26  6.674522  3.632702  2.867167  6.231740  ...  13.010423  5.954630   \n",
              "27  5.996500  4.597950  2.553556  7.399046  ...  13.542773  5.108145   \n",
              "28  6.387383  4.483243  2.675888  6.483243  ...  13.215435  5.711512   \n",
              "29  6.487776  4.435308  2.002349  6.757237  ...  12.910892  6.203983   \n",
              "30  6.300427  3.222424  3.052499  7.820684  ...  13.639105  6.181782   \n",
              "31  6.532257  3.543572  2.543572  6.244012  ...  12.589332  7.027388   \n",
              "32  5.863743  3.693818  4.015746  6.632417  ...  12.962360  7.015746   \n",
              "33  6.672063  7.233374  2.121865  6.184875  ...  12.568506  6.723901   \n",
              "34  6.827029  3.072142 -0.512821  5.962913  ...  12.804451  6.464459   \n",
              "35  6.490989  3.200312  2.714885  6.876772  ...  12.718262  6.107202   \n",
              "36  6.167733  3.548823  1.741468  6.478434  ...  13.036376  6.316377   \n",
              "37  6.137358  3.436918  2.758846  6.740699  ...  13.546014  5.626743   \n",
              "38  1.420214  3.420214  1.420214  6.464608  ...  12.967591  6.227569   \n",
              "39  6.696283  2.544280  2.374355  6.800620  ...  13.053065  6.493296   \n",
              "40  6.761828  3.954473  3.369510  6.142100  ...  13.460505  6.193939   \n",
              "41  6.256484  4.186094  1.864166  6.200450  ...  12.512344  6.050033   \n",
              "42  5.740496  4.274832  2.467477  6.859795  ...  12.996582  6.072339   \n",
              "43  6.785558  2.333431  2.622938  6.458127  ...  13.506622  6.485434   \n",
              "44  6.439688  2.384405  2.191760  5.892200  ...  13.361327  6.868221   \n",
              "45  6.257204  3.532311  2.362386  6.384754  ...  13.961543  6.939815   \n",
              "46  6.347589  8.188523  3.424757  6.331648  ...  13.368859  5.394383   \n",
              "47  5.989136  3.417594  2.832632  5.862379  ...  13.418690  6.794564   \n",
              "48  6.204623  3.882694  2.230618  7.217679  ...  13.189895  5.489352   \n",
              "49  5.983817  3.359326  2.096292  7.509073  ...  13.068841  5.474803   \n",
              "50  6.214815  2.913645  3.276215  6.296115  ...  12.906583  6.988933   \n",
              "51  4.320867  3.261973  3.136442  6.484365  ...  13.317933  5.846936   \n",
              "52  6.245478  5.378744  2.613209  6.648833  ...  13.701600  5.613209   \n",
              "53  5.987683  3.665755  2.817758  6.645577  ...  13.393865  5.955262   \n",
              "54  6.441498  2.716605  2.131643  6.500877  ...  12.981830  6.146593   \n",
              "55  0.359925  4.167280  3.681854  6.734965  ...  13.286777  6.786190   \n",
              "\n",
              "        SELL.    LAIR2.      CTSW.       C9.     IRGM.      CD74.   MAGEA4.  \\\n",
              "0   13.118603  7.043824   9.175069  4.154007  3.388472  12.846674  4.236469   \n",
              "1   13.123501  7.974999   8.149124  3.722859  4.410915  13.001566  3.360289   \n",
              "2   13.224038  7.975681   8.865628  3.508076  4.208515  13.334028  3.208515   \n",
              "3   13.000296  8.317813   9.390058  3.486872  4.430288  13.177541  3.245864   \n",
              "4   13.220104  8.230784   9.263751  3.717714  4.302676  12.241494  2.869717   \n",
              "5   13.482509  7.427089   8.831342  3.638034  4.357927  13.175253  3.135534   \n",
              "6   12.754317  7.962531   8.557967  3.254186  4.201719  12.477154  2.446831   \n",
              "7   13.651134  8.661894   7.954388  4.207154  4.487262  11.592092  3.569724   \n",
              "8   13.242088  7.572058   9.539794  3.719615  4.357045  13.291473  3.942008   \n",
              "9   13.916860  8.355165   9.013990  3.814972  3.908082  12.636215  3.715437   \n",
              "10  13.128929  7.361713   8.153908  3.682233  4.682233  12.885887  2.489588   \n",
              "11  13.654693  7.337980   8.561434  3.545422  4.059995  12.351396  3.438507   \n",
              "12  12.834357  8.103732   9.578301  3.510777  4.648280  12.662216  3.773811   \n",
              "13  13.890582  7.889655   9.096699  3.549805  4.357159  12.626175  3.424274   \n",
              "14  14.625808  7.880570   8.584177  4.888791  5.184247  13.153873  4.599284   \n",
              "15  12.998988  7.800568   9.253824  3.903327  4.488290  12.606885  3.488290   \n",
              "16  13.282057  8.226011   9.290583  2.661226  3.883619  13.277469  4.076264   \n",
              "17  13.082521  7.590668   8.747930  3.574367  3.436863  12.698723  3.114935   \n",
              "18  13.281315  8.473194  10.608091  3.277989  3.725448  13.728732  3.725448   \n",
              "19  13.289038  7.613239   9.900297  3.869078  4.006581  13.701256  3.354505   \n",
              "20  12.848386  7.792362   9.207987  3.778195  4.174123  12.944820  3.922584   \n",
              "21  14.523230  7.887732   8.946065  4.724794  5.201232  11.792754  4.008587   \n",
              "22  14.133841  8.417694   8.439720  4.202681  4.132292  13.370338  3.617719   \n",
              "23  13.032461  7.423219  10.338625  3.798728  3.728338  12.900141  3.991373   \n",
              "24  13.128706  7.309090   9.618232  4.309090  3.543555  13.385277  3.681059   \n",
              "25  13.001114  8.416975   9.021566  3.812113  4.812113  12.937268  2.905222   \n",
              "26  12.689260  8.064875   9.574526  3.452130  3.715164  12.891476  3.130202   \n",
              "27  13.028656  8.522223   9.061351  3.875484  3.801484  12.880828  3.253996   \n",
              "28  13.004339  8.467702   8.689351  3.813392  4.260851  12.572069  3.746278   \n",
              "29  13.652593  7.918826   8.812278  3.680421  4.203983  12.970440  3.850346   \n",
              "30  13.914556  7.793966   8.820684  4.444817  4.222424  12.900731  3.052499   \n",
              "31  13.049260  8.483151   8.515116  4.067134  4.450463  12.370716  3.713497   \n",
              "32  13.228931  7.916210   8.883642  4.568287  4.501173  13.362555  3.693818   \n",
              "33  12.941702  7.940219   8.978069  3.401973  4.121865  12.736312  3.014950   \n",
              "34  13.147509  7.730353   9.340489  3.072142  4.844731  12.973386  2.657104   \n",
              "35  13.118749  8.535064   8.540162  4.347153  4.602410  12.997046  3.916519   \n",
              "36  13.097920  7.418600   8.903020  3.741468  4.478434  13.019433  2.856945   \n",
              "37  13.314011  8.367656   9.446747  3.606843  4.080774  12.984174  3.137358   \n",
              "38  13.706772  7.629668   8.453637  4.227569  4.590139  13.017801  3.420214   \n",
              "39  12.820921  8.598357   8.593523  3.766672  4.328551  13.063916  2.959317   \n",
              "40  12.608910  7.361977   9.731454  3.691439  4.308110  13.154963  3.369510   \n",
              "41  12.963120  8.400219   9.657282  3.127201  4.712163  12.452131  3.127201   \n",
              "42  12.784136  7.783382   9.448569  4.341946  4.740496  12.719157  2.689870   \n",
              "43  12.457983  7.884605   9.353331  3.687068  4.333431  13.583795  3.411434   \n",
              "44  12.697288  8.129239   9.492930  3.291296  4.191760  13.731819  2.969368   \n",
              "45  13.087965  7.596006   8.960438  4.220367  4.220367  14.028166  3.269277   \n",
              "46  13.735843  7.540234   8.355494  4.232112  5.049248  12.714968  3.746685   \n",
              "47  13.377838  7.356194   9.604121  3.948109  4.247669  13.219931  2.707101   \n",
              "48  12.918493  8.275012   9.486658  4.067119  4.067119  13.202161  3.671190   \n",
              "49  13.469701  8.505683   8.774364  3.359326  4.297926  12.871573  1.774364   \n",
              "50  14.032586  7.106290   8.315743  4.193753  4.498607  12.926868  3.276215   \n",
              "51  13.735932  7.957781   8.866835  3.764473  4.136442  12.889355  3.764473   \n",
              "52  13.113254  8.942333   8.670660  4.198172  4.814843  13.032959  3.461206   \n",
              "53  13.194318  7.154042   7.995676  3.303185  3.955262  13.242974  3.080793   \n",
              "54  12.718795  8.311552   8.670802  3.453571  4.354035  12.725967  3.938998   \n",
              "55  13.936528  7.867720   8.192815  4.681854  4.167280  12.713348  4.060365   \n",
              "\n",
              "        CD3E.  \n",
              "0   10.238972  \n",
              "1   10.659497  \n",
              "2    9.541499  \n",
              "3   10.238673  \n",
              "4   10.687340  \n",
              "5   10.722374  \n",
              "6   10.672039  \n",
              "7    9.628618  \n",
              "8   10.893986  \n",
              "9   10.408924  \n",
              "10  11.253038  \n",
              "11  11.019997  \n",
              "12  11.253143  \n",
              "13  10.348546  \n",
              "14   8.204146  \n",
              "15  10.899377  \n",
              "16  11.077672  \n",
              "17  10.603779  \n",
              "18  10.561709  \n",
              "19  11.458916  \n",
              "20  11.280555  \n",
              "21   9.712984  \n",
              "22  10.347582  \n",
              "23  11.631316  \n",
              "24  11.130770  \n",
              "25  10.660944  \n",
              "26  11.250440  \n",
              "27  10.554964  \n",
              "28  11.111767  \n",
              "29  10.096163  \n",
              "30   9.703551  \n",
              "31  10.576307  \n",
              "32   9.989969  \n",
              "33  11.383625  \n",
              "34  11.524040  \n",
              "35  10.823932  \n",
              "36  11.172269  \n",
              "37  11.039617  \n",
              "38  10.980547  \n",
              "39  10.731357  \n",
              "40  11.410713  \n",
              "41  11.266752  \n",
              "42  10.555824  \n",
              "43  11.429707  \n",
              "44  11.415417  \n",
              "45  10.788651  \n",
              "46  10.866318  \n",
              "47  10.619990  \n",
              "48  10.443548  \n",
              "49   9.975262  \n",
              "50  10.786650  \n",
              "51  10.363511  \n",
              "52  10.527295  \n",
              "53  11.286179  \n",
              "54  10.858429  \n",
              "55  10.283253  \n",
              "\n",
              "[56 rows x 736 columns]"
            ],
            "text/html": [
              "\n",
              "  <div id=\"df-8a397da7-a6dd-4799-83d3-d08109a37fc6\">\n",
              "    <div class=\"colab-df-container\">\n",
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              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>Unnamed: 0</th>\n",
              "      <th>Sample.ID</th>\n",
              "      <th>Pair</th>\n",
              "      <th>Time</th>\n",
              "      <th>Response</th>\n",
              "      <th>IRF5.</th>\n",
              "      <th>ELK1.</th>\n",
              "      <th>C4BPA.</th>\n",
              "      <th>C7.</th>\n",
              "      <th>CASP10.</th>\n",
              "      <th>...</th>\n",
              "      <th>ANXA1.</th>\n",
              "      <th>POU2AF1.</th>\n",
              "      <th>SELL.</th>\n",
              "      <th>LAIR2.</th>\n",
              "      <th>CTSW.</th>\n",
              "      <th>C9.</th>\n",
              "      <th>IRGM.</th>\n",
              "      <th>CD74.</th>\n",
              "      <th>MAGEA4.</th>\n",
              "      <th>CD3E.</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>1</td>\n",
              "      <td>PA-180001</td>\n",
              "      <td>1</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>8.175069</td>\n",
              "      <td>6.351946</td>\n",
              "      <td>4.154007</td>\n",
              "      <td>2.651507</td>\n",
              "      <td>7.304949</td>\n",
              "      <td>...</td>\n",
              "      <td>13.044361</td>\n",
              "      <td>5.154007</td>\n",
              "      <td>13.118603</td>\n",
              "      <td>7.043824</td>\n",
              "      <td>9.175069</td>\n",
              "      <td>4.154007</td>\n",
              "      <td>3.388472</td>\n",
              "      <td>12.846674</td>\n",
              "      <td>4.236469</td>\n",
              "      <td>10.238972</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>2</td>\n",
              "      <td>PA-180013</td>\n",
              "      <td>7</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.897230</td>\n",
              "      <td>6.483671</td>\n",
              "      <td>3.253374</td>\n",
              "      <td>3.012365</td>\n",
              "      <td>6.619023</td>\n",
              "      <td>...</td>\n",
              "      <td>12.706644</td>\n",
              "      <td>6.970786</td>\n",
              "      <td>13.123501</td>\n",
              "      <td>7.974999</td>\n",
              "      <td>8.149124</td>\n",
              "      <td>3.722859</td>\n",
              "      <td>4.410915</td>\n",
              "      <td>13.001566</td>\n",
              "      <td>3.360289</td>\n",
              "      <td>10.659497</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>3</td>\n",
              "      <td>PA-180022</td>\n",
              "      <td>9</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.959287</td>\n",
              "      <td>6.353566</td>\n",
              "      <td>2.315431</td>\n",
              "      <td>2.830004</td>\n",
              "      <td>6.784200</td>\n",
              "      <td>...</td>\n",
              "      <td>12.859843</td>\n",
              "      <td>6.959287</td>\n",
              "      <td>13.224038</td>\n",
              "      <td>7.975681</td>\n",
              "      <td>8.865628</td>\n",
              "      <td>3.508076</td>\n",
              "      <td>4.208515</td>\n",
              "      <td>13.334028</td>\n",
              "      <td>3.208515</td>\n",
              "      <td>9.541499</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>4</td>\n",
              "      <td>PA-180044</td>\n",
              "      <td>14</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>8.094771</td>\n",
              "      <td>6.567792</td>\n",
              "      <td>7.465912</td>\n",
              "      <td>3.108360</td>\n",
              "      <td>6.705295</td>\n",
              "      <td>...</td>\n",
              "      <td>13.300776</td>\n",
              "      <td>6.161471</td>\n",
              "      <td>13.000296</td>\n",
              "      <td>8.317813</td>\n",
              "      <td>9.390058</td>\n",
              "      <td>3.486872</td>\n",
              "      <td>4.430288</td>\n",
              "      <td>13.177541</td>\n",
              "      <td>3.245864</td>\n",
              "      <td>10.238673</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>5</td>\n",
              "      <td>PA-180062</td>\n",
              "      <td>17</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.712696</td>\n",
              "      <td>5.380679</td>\n",
              "      <td>2.869717</td>\n",
              "      <td>2.717714</td>\n",
              "      <td>6.851570</td>\n",
              "      <td>...</td>\n",
              "      <td>12.977980</td>\n",
              "      <td>6.262034</td>\n",
              "      <td>13.220104</td>\n",
              "      <td>8.230784</td>\n",
              "      <td>9.263751</td>\n",
              "      <td>3.717714</td>\n",
              "      <td>4.302676</td>\n",
              "      <td>12.241494</td>\n",
              "      <td>2.869717</td>\n",
              "      <td>10.687340</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5</th>\n",
              "      <td>6</td>\n",
              "      <td>PA-180065</td>\n",
              "      <td>19</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.985200</td>\n",
              "      <td>6.264817</td>\n",
              "      <td>2.550572</td>\n",
              "      <td>2.550572</td>\n",
              "      <td>6.740396</td>\n",
              "      <td>...</td>\n",
              "      <td>13.239368</td>\n",
              "      <td>5.408553</td>\n",
              "      <td>13.482509</td>\n",
              "      <td>7.427089</td>\n",
              "      <td>8.831342</td>\n",
              "      <td>3.638034</td>\n",
              "      <td>4.357927</td>\n",
              "      <td>13.175253</td>\n",
              "      <td>3.135534</td>\n",
              "      <td>10.722374</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>6</th>\n",
              "      <td>7</td>\n",
              "      <td>PA-180107</td>\n",
              "      <td>24</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.830536</td>\n",
              "      <td>6.147271</td>\n",
              "      <td>1.446831</td>\n",
              "      <td>2.616756</td>\n",
              "      <td>6.685236</td>\n",
              "      <td>...</td>\n",
              "      <td>12.737570</td>\n",
              "      <td>6.001420</td>\n",
              "      <td>12.754317</td>\n",
              "      <td>7.962531</td>\n",
              "      <td>8.557967</td>\n",
              "      <td>3.254186</td>\n",
              "      <td>4.201719</td>\n",
              "      <td>12.477154</td>\n",
              "      <td>2.446831</td>\n",
              "      <td>10.672039</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7</th>\n",
              "      <td>8</td>\n",
              "      <td>PA-190147</td>\n",
              "      <td>32</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.141266</td>\n",
              "      <td>0.399799</td>\n",
              "      <td>3.207154</td>\n",
              "      <td>2.984762</td>\n",
              "      <td>6.859231</td>\n",
              "      <td>...</td>\n",
              "      <td>13.556515</td>\n",
              "      <td>6.422167</td>\n",
              "      <td>13.651134</td>\n",
              "      <td>8.661894</td>\n",
              "      <td>7.954388</td>\n",
              "      <td>4.207154</td>\n",
              "      <td>4.487262</td>\n",
              "      <td>11.592092</td>\n",
              "      <td>3.569724</td>\n",
              "      <td>9.628618</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>8</th>\n",
              "      <td>9</td>\n",
              "      <td>PA-190170</td>\n",
              "      <td>34</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.937708</td>\n",
              "      <td>6.604973</td>\n",
              "      <td>3.134653</td>\n",
              "      <td>2.549690</td>\n",
              "      <td>6.825815</td>\n",
              "      <td>...</td>\n",
              "      <td>13.564844</td>\n",
              "      <td>5.889540</td>\n",
              "      <td>13.242088</td>\n",
              "      <td>7.572058</td>\n",
              "      <td>9.539794</td>\n",
              "      <td>3.719615</td>\n",
              "      <td>4.357045</td>\n",
              "      <td>13.291473</td>\n",
              "      <td>3.942008</td>\n",
              "      <td>10.893986</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>9</th>\n",
              "      <td>10</td>\n",
              "      <td>PA-190190</td>\n",
              "      <td>36</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.873866</td>\n",
              "      <td>5.431644</td>\n",
              "      <td>3.367513</td>\n",
              "      <td>2.230010</td>\n",
              "      <td>6.580507</td>\n",
              "      <td>...</td>\n",
              "      <td>13.009729</td>\n",
              "      <td>5.580507</td>\n",
              "      <td>13.916860</td>\n",
              "      <td>8.355165</td>\n",
              "      <td>9.013990</td>\n",
              "      <td>3.814972</td>\n",
              "      <td>3.908082</td>\n",
              "      <td>12.636215</td>\n",
              "      <td>3.715437</td>\n",
              "      <td>10.408924</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>10</th>\n",
              "      <td>11</td>\n",
              "      <td>PA-190223</td>\n",
              "      <td>38</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>8.178088</td>\n",
              "      <td>6.842104</td>\n",
              "      <td>7.618871</td>\n",
              "      <td>2.489588</td>\n",
              "      <td>6.748322</td>\n",
              "      <td>...</td>\n",
              "      <td>13.212152</td>\n",
              "      <td>6.074551</td>\n",
              "      <td>13.128929</td>\n",
              "      <td>7.361713</td>\n",
              "      <td>8.153908</td>\n",
              "      <td>3.682233</td>\n",
              "      <td>4.682233</td>\n",
              "      <td>12.885887</td>\n",
              "      <td>2.489588</td>\n",
              "      <td>11.253038</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>11</th>\n",
              "      <td>12</td>\n",
              "      <td>PA-190254</td>\n",
              "      <td>43</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.459166</td>\n",
              "      <td>6.213801</td>\n",
              "      <td>3.985995</td>\n",
              "      <td>2.323030</td>\n",
              "      <td>6.410493</td>\n",
              "      <td>...</td>\n",
              "      <td>12.936666</td>\n",
              "      <td>5.966886</td>\n",
              "      <td>13.654693</td>\n",
              "      <td>7.337980</td>\n",
              "      <td>8.561434</td>\n",
              "      <td>3.545422</td>\n",
              "      <td>4.059995</td>\n",
              "      <td>12.351396</td>\n",
              "      <td>3.438507</td>\n",
              "      <td>11.019997</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>12</th>\n",
              "      <td>13</td>\n",
              "      <td>PA-190308</td>\n",
              "      <td>44</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.592571</td>\n",
              "      <td>6.558083</td>\n",
              "      <td>8.087702</td>\n",
              "      <td>2.411241</td>\n",
              "      <td>6.233243</td>\n",
              "      <td>...</td>\n",
              "      <td>12.954549</td>\n",
              "      <td>5.581166</td>\n",
              "      <td>12.834357</td>\n",
              "      <td>8.103732</td>\n",
              "      <td>9.578301</td>\n",
              "      <td>3.510777</td>\n",
              "      <td>4.648280</td>\n",
              "      <td>12.662216</td>\n",
              "      <td>3.773811</td>\n",
              "      <td>11.253143</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>13</th>\n",
              "      <td>14</td>\n",
              "      <td>PA-190313</td>\n",
              "      <td>45</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.992748</td>\n",
              "      <td>6.440575</td>\n",
              "      <td>3.964842</td>\n",
              "      <td>3.134767</td>\n",
              "      <td>6.692762</td>\n",
              "      <td>...</td>\n",
              "      <td>13.184767</td>\n",
              "      <td>5.665282</td>\n",
              "      <td>13.890582</td>\n",
              "      <td>7.889655</td>\n",
              "      <td>9.096699</td>\n",
              "      <td>3.549805</td>\n",
              "      <td>4.357159</td>\n",
              "      <td>12.626175</td>\n",
              "      <td>3.424274</td>\n",
              "      <td>10.348546</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>14</th>\n",
              "      <td>15</td>\n",
              "      <td>PA-190414</td>\n",
              "      <td>46</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>8.589231</td>\n",
              "      <td>5.184247</td>\n",
              "      <td>6.236714</td>\n",
              "      <td>2.751287</td>\n",
              "      <td>7.558642</td>\n",
              "      <td>...</td>\n",
              "      <td>13.439538</td>\n",
              "      <td>5.638813</td>\n",
              "      <td>14.625808</td>\n",
              "      <td>7.880570</td>\n",
              "      <td>8.584177</td>\n",
              "      <td>4.888791</td>\n",
              "      <td>5.184247</td>\n",
              "      <td>13.153873</td>\n",
              "      <td>4.599284</td>\n",
              "      <td>8.204146</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>15</th>\n",
              "      <td>16</td>\n",
              "      <td>PA-190572</td>\n",
              "      <td>53</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.731146</td>\n",
              "      <td>6.414289</td>\n",
              "      <td>3.829327</td>\n",
              "      <td>2.751324</td>\n",
              "      <td>6.658215</td>\n",
              "      <td>...</td>\n",
              "      <td>12.865645</td>\n",
              "      <td>5.388754</td>\n",
              "      <td>12.998988</td>\n",
              "      <td>7.800568</td>\n",
              "      <td>9.253824</td>\n",
              "      <td>3.903327</td>\n",
              "      <td>4.488290</td>\n",
              "      <td>12.606885</td>\n",
              "      <td>3.488290</td>\n",
              "      <td>10.899377</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>16</th>\n",
              "      <td>17</td>\n",
              "      <td>PA-190680</td>\n",
              "      <td>57</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>8.131546</td>\n",
              "      <td>6.857624</td>\n",
              "      <td>3.398192</td>\n",
              "      <td>3.398192</td>\n",
              "      <td>6.983154</td>\n",
              "      <td>...</td>\n",
              "      <td>13.237711</td>\n",
              "      <td>6.720120</td>\n",
              "      <td>13.282057</td>\n",
              "      <td>8.226011</td>\n",
              "      <td>9.290583</td>\n",
              "      <td>2.661226</td>\n",
              "      <td>3.883619</td>\n",
              "      <td>13.277469</td>\n",
              "      <td>4.076264</td>\n",
              "      <td>11.077672</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>17</th>\n",
              "      <td>18</td>\n",
              "      <td>PA-200719</td>\n",
              "      <td>58</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.489974</td>\n",
              "      <td>6.284860</td>\n",
              "      <td>3.574367</td>\n",
              "      <td>2.114935</td>\n",
              "      <td>6.829180</td>\n",
              "      <td>...</td>\n",
              "      <td>12.832611</td>\n",
              "      <td>5.507252</td>\n",
              "      <td>13.082521</td>\n",
              "      <td>7.590668</td>\n",
              "      <td>8.747930</td>\n",
              "      <td>3.574367</td>\n",
              "      <td>3.436863</td>\n",
              "      <td>12.698723</td>\n",
              "      <td>3.114935</td>\n",
              "      <td>10.603779</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>18</th>\n",
              "      <td>19</td>\n",
              "      <td>PA-201112</td>\n",
              "      <td>70</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>8.090021</td>\n",
              "      <td>6.476769</td>\n",
              "      <td>4.573445</td>\n",
              "      <td>2.988483</td>\n",
              "      <td>6.403520</td>\n",
              "      <td>...</td>\n",
              "      <td>13.223699</td>\n",
              "      <td>6.462414</td>\n",
              "      <td>13.281315</td>\n",
              "      <td>8.473194</td>\n",
              "      <td>10.608091</td>\n",
              "      <td>3.277989</td>\n",
              "      <td>3.725448</td>\n",
              "      <td>13.728732</td>\n",
              "      <td>3.725448</td>\n",
              "      <td>10.561709</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>19</th>\n",
              "      <td>20</td>\n",
              "      <td>PA-201145</td>\n",
              "      <td>71</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>8.097897</td>\n",
              "      <td>6.441967</td>\n",
              "      <td>2.547150</td>\n",
              "      <td>3.354505</td>\n",
              "      <td>6.441967</td>\n",
              "      <td>...</td>\n",
              "      <td>12.975379</td>\n",
              "      <td>6.392640</td>\n",
              "      <td>13.289038</td>\n",
              "      <td>7.613239</td>\n",
              "      <td>9.900297</td>\n",
              "      <td>3.869078</td>\n",
              "      <td>4.006581</td>\n",
              "      <td>13.701256</td>\n",
              "      <td>3.354505</td>\n",
              "      <td>11.458916</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>20</th>\n",
              "      <td>21</td>\n",
              "      <td>PA-201162</td>\n",
              "      <td>72</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.690138</td>\n",
              "      <td>6.472782</td>\n",
              "      <td>3.530267</td>\n",
              "      <td>2.530267</td>\n",
              "      <td>6.363157</td>\n",
              "      <td>...</td>\n",
              "      <td>12.915860</td>\n",
              "      <td>5.922584</td>\n",
              "      <td>12.848386</td>\n",
              "      <td>7.792362</td>\n",
              "      <td>9.207987</td>\n",
              "      <td>3.778195</td>\n",
              "      <td>4.174123</td>\n",
              "      <td>12.944820</td>\n",
              "      <td>3.922584</td>\n",
              "      <td>11.280555</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>21</th>\n",
              "      <td>22</td>\n",
              "      <td>PA-201182</td>\n",
              "      <td>73</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.108122</td>\n",
              "      <td>6.059213</td>\n",
              "      <td>4.956119</td>\n",
              "      <td>3.371157</td>\n",
              "      <td>6.288694</td>\n",
              "      <td>...</td>\n",
              "      <td>13.098699</td>\n",
              "      <td>5.660663</td>\n",
              "      <td>14.523230</td>\n",
              "      <td>7.887732</td>\n",
              "      <td>8.946065</td>\n",
              "      <td>4.724794</td>\n",
              "      <td>5.201232</td>\n",
              "      <td>11.792754</td>\n",
              "      <td>4.008587</td>\n",
              "      <td>9.712984</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>22</th>\n",
              "      <td>23</td>\n",
              "      <td>PA-201237</td>\n",
              "      <td>76</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>8.053538</td>\n",
              "      <td>4.333926</td>\n",
              "      <td>5.454220</td>\n",
              "      <td>1.810364</td>\n",
              "      <td>6.918888</td>\n",
              "      <td>...</td>\n",
              "      <td>13.838011</td>\n",
              "      <td>5.960111</td>\n",
              "      <td>14.133841</td>\n",
              "      <td>8.417694</td>\n",
              "      <td>8.439720</td>\n",
              "      <td>4.202681</td>\n",
              "      <td>4.132292</td>\n",
              "      <td>13.370338</td>\n",
              "      <td>3.617719</td>\n",
              "      <td>10.347582</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>23</th>\n",
              "      <td>24</td>\n",
              "      <td>PA-201291</td>\n",
              "      <td>77</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.596235</td>\n",
              "      <td>6.654338</td>\n",
              "      <td>4.264391</td>\n",
              "      <td>3.313301</td>\n",
              "      <td>6.106850</td>\n",
              "      <td>...</td>\n",
              "      <td>13.109449</td>\n",
              "      <td>6.276775</td>\n",
              "      <td>13.032461</td>\n",
              "      <td>7.423219</td>\n",
              "      <td>10.338625</td>\n",
              "      <td>3.798728</td>\n",
              "      <td>3.728338</td>\n",
              "      <td>12.900141</td>\n",
              "      <td>3.991373</td>\n",
              "      <td>11.631316</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>24</th>\n",
              "      <td>25</td>\n",
              "      <td>PA-211459</td>\n",
              "      <td>79</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>8.215981</td>\n",
              "      <td>5.806590</td>\n",
              "      <td>2.543555</td>\n",
              "      <td>3.681059</td>\n",
              "      <td>6.760786</td>\n",
              "      <td>...</td>\n",
              "      <td>13.220570</td>\n",
              "      <td>5.745189</td>\n",
              "      <td>13.128706</td>\n",
              "      <td>7.309090</td>\n",
              "      <td>9.618232</td>\n",
              "      <td>4.309090</td>\n",
              "      <td>3.543555</td>\n",
              "      <td>13.385277</td>\n",
              "      <td>3.681059</td>\n",
              "      <td>11.130770</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>25</th>\n",
              "      <td>26</td>\n",
              "      <td>PA-180030</td>\n",
              "      <td>10</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>8.376898</td>\n",
              "      <td>6.812113</td>\n",
              "      <td>3.364654</td>\n",
              "      <td>2.227150</td>\n",
              "      <td>7.085131</td>\n",
              "      <td>...</td>\n",
              "      <td>12.676299</td>\n",
              "      <td>6.646689</td>\n",
              "      <td>13.001114</td>\n",
              "      <td>8.416975</td>\n",
              "      <td>9.021566</td>\n",
              "      <td>3.812113</td>\n",
              "      <td>4.812113</td>\n",
              "      <td>12.937268</td>\n",
              "      <td>2.905222</td>\n",
              "      <td>10.660944</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>26</th>\n",
              "      <td>27</td>\n",
              "      <td>PA-180039</td>\n",
              "      <td>12</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.730115</td>\n",
              "      <td>6.674522</td>\n",
              "      <td>3.632702</td>\n",
              "      <td>2.867167</td>\n",
              "      <td>6.231740</td>\n",
              "      <td>...</td>\n",
              "      <td>13.010423</td>\n",
              "      <td>5.954630</td>\n",
              "      <td>12.689260</td>\n",
              "      <td>8.064875</td>\n",
              "      <td>9.574526</td>\n",
              "      <td>3.452130</td>\n",
              "      <td>3.715164</td>\n",
              "      <td>12.891476</td>\n",
              "      <td>3.130202</td>\n",
              "      <td>11.250440</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>27</th>\n",
              "      <td>28</td>\n",
              "      <td>PA-180063</td>\n",
              "      <td>18</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>8.004767</td>\n",
              "      <td>5.996500</td>\n",
              "      <td>4.597950</td>\n",
              "      <td>2.553556</td>\n",
              "      <td>7.399046</td>\n",
              "      <td>...</td>\n",
              "      <td>13.542773</td>\n",
              "      <td>5.108145</td>\n",
              "      <td>13.028656</td>\n",
              "      <td>8.522223</td>\n",
              "      <td>9.061351</td>\n",
              "      <td>3.875484</td>\n",
              "      <td>3.801484</td>\n",
              "      <td>12.880828</td>\n",
              "      <td>3.253996</td>\n",
              "      <td>10.554964</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>28</th>\n",
              "      <td>29</td>\n",
              "      <td>PA-180072</td>\n",
              "      <td>20</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.403809</td>\n",
              "      <td>6.387383</td>\n",
              "      <td>4.483243</td>\n",
              "      <td>2.675888</td>\n",
              "      <td>6.483243</td>\n",
              "      <td>...</td>\n",
              "      <td>13.215435</td>\n",
              "      <td>5.711512</td>\n",
              "      <td>13.004339</td>\n",
              "      <td>8.467702</td>\n",
              "      <td>8.689351</td>\n",
              "      <td>3.813392</td>\n",
              "      <td>4.260851</td>\n",
              "      <td>12.572069</td>\n",
              "      <td>3.746278</td>\n",
              "      <td>11.111767</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>29</th>\n",
              "      <td>30</td>\n",
              "      <td>PA-180092</td>\n",
              "      <td>23</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>8.127504</td>\n",
              "      <td>6.487776</td>\n",
              "      <td>4.435308</td>\n",
              "      <td>2.002349</td>\n",
              "      <td>6.757237</td>\n",
              "      <td>...</td>\n",
              "      <td>12.910892</td>\n",
              "      <td>6.203983</td>\n",
              "      <td>13.652593</td>\n",
              "      <td>7.918826</td>\n",
              "      <td>8.812278</td>\n",
              "      <td>3.680421</td>\n",
              "      <td>4.203983</td>\n",
              "      <td>12.970440</td>\n",
              "      <td>3.850346</td>\n",
              "      <td>10.096163</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>30</th>\n",
              "      <td>31</td>\n",
              "      <td>PA-190135</td>\n",
              "      <td>27</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>8.907368</td>\n",
              "      <td>6.300427</td>\n",
              "      <td>3.222424</td>\n",
              "      <td>3.052499</td>\n",
              "      <td>7.820684</td>\n",
              "      <td>...</td>\n",
              "      <td>13.639105</td>\n",
              "      <td>6.181782</td>\n",
              "      <td>13.914556</td>\n",
              "      <td>7.793966</td>\n",
              "      <td>8.820684</td>\n",
              "      <td>4.444817</td>\n",
              "      <td>4.222424</td>\n",
              "      <td>12.900731</td>\n",
              "      <td>3.052499</td>\n",
              "      <td>9.703551</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>31</th>\n",
              "      <td>32</td>\n",
              "      <td>PA-190136</td>\n",
              "      <td>28</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.753025</td>\n",
              "      <td>6.532257</td>\n",
              "      <td>3.543572</td>\n",
              "      <td>2.543572</td>\n",
              "      <td>6.244012</td>\n",
              "      <td>...</td>\n",
              "      <td>12.589332</td>\n",
              "      <td>7.027388</td>\n",
              "      <td>13.049260</td>\n",
              "      <td>8.483151</td>\n",
              "      <td>8.515116</td>\n",
              "      <td>4.067134</td>\n",
              "      <td>4.450463</td>\n",
              "      <td>12.370716</td>\n",
              "      <td>3.713497</td>\n",
              "      <td>10.576307</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>32</th>\n",
              "      <td>33</td>\n",
              "      <td>PA-190142</td>\n",
              "      <td>31</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>8.191004</td>\n",
              "      <td>5.863743</td>\n",
              "      <td>3.693818</td>\n",
              "      <td>4.015746</td>\n",
              "      <td>6.632417</td>\n",
              "      <td>...</td>\n",
              "      <td>12.962360</td>\n",
              "      <td>7.015746</td>\n",
              "      <td>13.228931</td>\n",
              "      <td>7.916210</td>\n",
              "      <td>8.883642</td>\n",
              "      <td>4.568287</td>\n",
              "      <td>4.501173</td>\n",
              "      <td>13.362555</td>\n",
              "      <td>3.693818</td>\n",
              "      <td>9.989969</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>33</th>\n",
              "      <td>34</td>\n",
              "      <td>PA-150167</td>\n",
              "      <td>33</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.443794</td>\n",
              "      <td>6.672063</td>\n",
              "      <td>7.233374</td>\n",
              "      <td>2.121865</td>\n",
              "      <td>6.184875</td>\n",
              "      <td>...</td>\n",
              "      <td>12.568506</td>\n",
              "      <td>6.723901</td>\n",
              "      <td>12.941702</td>\n",
              "      <td>7.940219</td>\n",
              "      <td>8.978069</td>\n",
              "      <td>3.401973</td>\n",
              "      <td>4.121865</td>\n",
              "      <td>12.736312</td>\n",
              "      <td>3.014950</td>\n",
              "      <td>11.383625</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>34</th>\n",
              "      <td>35</td>\n",
              "      <td>PA-190172</td>\n",
              "      <td>35</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.423817</td>\n",
              "      <td>6.827029</td>\n",
              "      <td>3.072142</td>\n",
              "      <td>-0.512821</td>\n",
              "      <td>5.962913</td>\n",
              "      <td>...</td>\n",
              "      <td>12.804451</td>\n",
              "      <td>6.464459</td>\n",
              "      <td>13.147509</td>\n",
              "      <td>7.730353</td>\n",
              "      <td>9.340489</td>\n",
              "      <td>3.072142</td>\n",
              "      <td>4.844731</td>\n",
              "      <td>12.973386</td>\n",
              "      <td>2.657104</td>\n",
              "      <td>11.524040</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>35</th>\n",
              "      <td>36</td>\n",
              "      <td>PA-190415</td>\n",
              "      <td>47</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>8.244706</td>\n",
              "      <td>6.490989</td>\n",
              "      <td>3.200312</td>\n",
              "      <td>2.714885</td>\n",
              "      <td>6.876772</td>\n",
              "      <td>...</td>\n",
              "      <td>12.718262</td>\n",
              "      <td>6.107202</td>\n",
              "      <td>13.118749</td>\n",
              "      <td>8.535064</td>\n",
              "      <td>8.540162</td>\n",
              "      <td>4.347153</td>\n",
              "      <td>4.602410</td>\n",
              "      <td>12.997046</td>\n",
              "      <td>3.916519</td>\n",
              "      <td>10.823932</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>36</th>\n",
              "      <td>37</td>\n",
              "      <td>PA-190534</td>\n",
              "      <td>51</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.796751</td>\n",
              "      <td>6.167733</td>\n",
              "      <td>3.548823</td>\n",
              "      <td>1.741468</td>\n",
              "      <td>6.478434</td>\n",
              "      <td>...</td>\n",
              "      <td>13.036376</td>\n",
              "      <td>6.316377</td>\n",
              "      <td>13.097920</td>\n",
              "      <td>7.418600</td>\n",
              "      <td>8.903020</td>\n",
              "      <td>3.741468</td>\n",
              "      <td>4.478434</td>\n",
              "      <td>13.019433</td>\n",
              "      <td>2.856945</td>\n",
              "      <td>11.172269</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>37</th>\n",
              "      <td>38</td>\n",
              "      <td>PA-190625</td>\n",
              "      <td>55</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>8.087970</td>\n",
              "      <td>6.137358</td>\n",
              "      <td>3.436918</td>\n",
              "      <td>2.758846</td>\n",
              "      <td>6.740699</td>\n",
              "      <td>...</td>\n",
              "      <td>13.546014</td>\n",
              "      <td>5.626743</td>\n",
              "      <td>13.314011</td>\n",
              "      <td>8.367656</td>\n",
              "      <td>9.446747</td>\n",
              "      <td>3.606843</td>\n",
              "      <td>4.080774</td>\n",
              "      <td>12.984174</td>\n",
              "      <td>3.137358</td>\n",
              "      <td>11.039617</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>38</th>\n",
              "      <td>39</td>\n",
              "      <td>PA-200787</td>\n",
              "      <td>60</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>8.374411</td>\n",
              "      <td>1.420214</td>\n",
              "      <td>3.420214</td>\n",
              "      <td>1.420214</td>\n",
              "      <td>6.464608</td>\n",
              "      <td>...</td>\n",
              "      <td>12.967591</td>\n",
              "      <td>6.227569</td>\n",
              "      <td>13.706772</td>\n",
              "      <td>7.629668</td>\n",
              "      <td>8.453637</td>\n",
              "      <td>4.227569</td>\n",
              "      <td>4.590139</td>\n",
              "      <td>13.017801</td>\n",
              "      <td>3.420214</td>\n",
              "      <td>10.980547</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>39</th>\n",
              "      <td>40</td>\n",
              "      <td>PA-200851</td>\n",
              "      <td>63</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.804807</td>\n",
              "      <td>6.696283</td>\n",
              "      <td>2.544280</td>\n",
              "      <td>2.374355</td>\n",
              "      <td>6.800620</td>\n",
              "      <td>...</td>\n",
              "      <td>13.053065</td>\n",
              "      <td>6.493296</td>\n",
              "      <td>12.820921</td>\n",
              "      <td>8.598357</td>\n",
              "      <td>8.593523</td>\n",
              "      <td>3.766672</td>\n",
              "      <td>4.328551</td>\n",
              "      <td>13.063916</td>\n",
              "      <td>2.959317</td>\n",
              "      <td>10.731357</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>40</th>\n",
              "      <td>41</td>\n",
              "      <td>PA-200997</td>\n",
              "      <td>65</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.929206</td>\n",
              "      <td>6.761828</td>\n",
              "      <td>3.954473</td>\n",
              "      <td>3.369510</td>\n",
              "      <td>6.142100</td>\n",
              "      <td>...</td>\n",
              "      <td>13.460505</td>\n",
              "      <td>6.193939</td>\n",
              "      <td>12.608910</td>\n",
              "      <td>7.361977</td>\n",
              "      <td>9.731454</td>\n",
              "      <td>3.691439</td>\n",
              "      <td>4.308110</td>\n",
              "      <td>13.154963</td>\n",
              "      <td>3.369510</td>\n",
              "      <td>11.410713</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>41</th>\n",
              "      <td>42</td>\n",
              "      <td>PA-201007</td>\n",
              "      <td>66</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.323598</td>\n",
              "      <td>6.256484</td>\n",
              "      <td>4.186094</td>\n",
              "      <td>1.864166</td>\n",
              "      <td>6.200450</td>\n",
              "      <td>...</td>\n",
              "      <td>12.512344</td>\n",
              "      <td>6.050033</td>\n",
              "      <td>12.963120</td>\n",
              "      <td>8.400219</td>\n",
              "      <td>9.657282</td>\n",
              "      <td>3.127201</td>\n",
              "      <td>4.712163</td>\n",
              "      <td>12.452131</td>\n",
              "      <td>3.127201</td>\n",
              "      <td>11.266752</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>42</th>\n",
              "      <td>43</td>\n",
              "      <td>PA-201070</td>\n",
              "      <td>67</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>8.130442</td>\n",
              "      <td>5.740496</td>\n",
              "      <td>4.274832</td>\n",
              "      <td>2.467477</td>\n",
              "      <td>6.859795</td>\n",
              "      <td>...</td>\n",
              "      <td>12.996582</td>\n",
              "      <td>6.072339</td>\n",
              "      <td>12.784136</td>\n",
              "      <td>7.783382</td>\n",
              "      <td>9.448569</td>\n",
              "      <td>4.341946</td>\n",
              "      <td>4.740496</td>\n",
              "      <td>12.719157</td>\n",
              "      <td>2.689870</td>\n",
              "      <td>10.555824</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>43</th>\n",
              "      <td>44</td>\n",
              "      <td>PA-201079</td>\n",
              "      <td>68</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>8.085347</td>\n",
              "      <td>6.785558</td>\n",
              "      <td>2.333431</td>\n",
              "      <td>2.622938</td>\n",
              "      <td>6.458127</td>\n",
              "      <td>...</td>\n",
              "      <td>13.506622</td>\n",
              "      <td>6.485434</td>\n",
              "      <td>12.457983</td>\n",
              "      <td>7.884605</td>\n",
              "      <td>9.353331</td>\n",
              "      <td>3.687068</td>\n",
              "      <td>4.333431</td>\n",
              "      <td>13.583795</td>\n",
              "      <td>3.411434</td>\n",
              "      <td>11.429707</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>44</th>\n",
              "      <td>45</td>\n",
              "      <td>PA-201186</td>\n",
              "      <td>74</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.823197</td>\n",
              "      <td>6.439688</td>\n",
              "      <td>2.384405</td>\n",
              "      <td>2.191760</td>\n",
              "      <td>5.892200</td>\n",
              "      <td>...</td>\n",
              "      <td>13.361327</td>\n",
              "      <td>6.868221</td>\n",
              "      <td>12.697288</td>\n",
              "      <td>8.129239</td>\n",
              "      <td>9.492930</td>\n",
              "      <td>3.291296</td>\n",
              "      <td>4.191760</td>\n",
              "      <td>13.731819</td>\n",
              "      <td>2.969368</td>\n",
              "      <td>11.415417</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>45</th>\n",
              "      <td>46</td>\n",
              "      <td>PA-201217</td>\n",
              "      <td>75</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>8.103853</td>\n",
              "      <td>6.257204</td>\n",
              "      <td>3.532311</td>\n",
              "      <td>2.362386</td>\n",
              "      <td>6.384754</td>\n",
              "      <td>...</td>\n",
              "      <td>13.961543</td>\n",
              "      <td>6.939815</td>\n",
              "      <td>13.087965</td>\n",
              "      <td>7.596006</td>\n",
              "      <td>8.960438</td>\n",
              "      <td>4.220367</td>\n",
              "      <td>4.220367</td>\n",
              "      <td>14.028166</td>\n",
              "      <td>3.269277</td>\n",
              "      <td>10.788651</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>46</th>\n",
              "      <td>47</td>\n",
              "      <td>PA-201357</td>\n",
              "      <td>78</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.574504</td>\n",
              "      <td>6.347589</td>\n",
              "      <td>8.188523</td>\n",
              "      <td>3.424757</td>\n",
              "      <td>6.331648</td>\n",
              "      <td>...</td>\n",
              "      <td>13.368859</td>\n",
              "      <td>5.394383</td>\n",
              "      <td>13.735843</td>\n",
              "      <td>7.540234</td>\n",
              "      <td>8.355494</td>\n",
              "      <td>4.232112</td>\n",
              "      <td>5.049248</td>\n",
              "      <td>12.714968</td>\n",
              "      <td>3.746685</td>\n",
              "      <td>10.866318</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>47</th>\n",
              "      <td>48</td>\n",
              "      <td>PA-211498</td>\n",
              "      <td>80</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Disease Control</td>\n",
              "      <td>7.965346</td>\n",
              "      <td>5.989136</td>\n",
              "      <td>3.417594</td>\n",
              "      <td>2.832632</td>\n",
              "      <td>5.862379</td>\n",
              "      <td>...</td>\n",
              "      <td>13.418690</td>\n",
              "      <td>6.794564</td>\n",
              "      <td>13.377838</td>\n",
              "      <td>7.356194</td>\n",
              "      <td>9.604121</td>\n",
              "      <td>3.948109</td>\n",
              "      <td>4.247669</td>\n",
              "      <td>13.219931</td>\n",
              "      <td>2.707101</td>\n",
              "      <td>10.619990</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>48</th>\n",
              "      <td>98</td>\n",
              "      <td>PA-180055</td>\n",
              "      <td>15</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Progressive Disease</td>\n",
              "      <td>8.442854</td>\n",
              "      <td>6.204623</td>\n",
              "      <td>3.882694</td>\n",
              "      <td>2.230618</td>\n",
              "      <td>7.217679</td>\n",
              "      <td>...</td>\n",
              "      <td>13.189895</td>\n",
              "      <td>5.489352</td>\n",
              "      <td>12.918493</td>\n",
              "      <td>8.275012</td>\n",
              "      <td>9.486658</td>\n",
              "      <td>4.067119</td>\n",
              "      <td>4.067119</td>\n",
              "      <td>13.202161</td>\n",
              "      <td>3.671190</td>\n",
              "      <td>10.443548</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>49</th>\n",
              "      <td>99</td>\n",
              "      <td>PA-180089</td>\n",
              "      <td>22</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Progressive Disease</td>\n",
              "      <td>8.045827</td>\n",
              "      <td>5.983817</td>\n",
              "      <td>3.359326</td>\n",
              "      <td>2.096292</td>\n",
              "      <td>7.509073</td>\n",
              "      <td>...</td>\n",
              "      <td>13.068841</td>\n",
              "      <td>5.474803</td>\n",
              "      <td>13.469701</td>\n",
              "      <td>8.505683</td>\n",
              "      <td>8.774364</td>\n",
              "      <td>3.359326</td>\n",
              "      <td>4.297926</td>\n",
              "      <td>12.871573</td>\n",
              "      <td>1.774364</td>\n",
              "      <td>9.975262</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>50</th>\n",
              "      <td>100</td>\n",
              "      <td>PA-190228</td>\n",
              "      <td>39</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Progressive Disease</td>\n",
              "      <td>7.668532</td>\n",
              "      <td>6.214815</td>\n",
              "      <td>2.913645</td>\n",
              "      <td>3.276215</td>\n",
              "      <td>6.296115</td>\n",
              "      <td>...</td>\n",
              "      <td>12.906583</td>\n",
              "      <td>6.988933</td>\n",
              "      <td>14.032586</td>\n",
              "      <td>7.106290</td>\n",
              "      <td>8.315743</td>\n",
              "      <td>4.193753</td>\n",
              "      <td>4.498607</td>\n",
              "      <td>12.926868</td>\n",
              "      <td>3.276215</td>\n",
              "      <td>10.786650</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>51</th>\n",
              "      <td>101</td>\n",
              "      <td>PA-201092</td>\n",
              "      <td>69</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Progressive Disease</td>\n",
              "      <td>8.196647</td>\n",
              "      <td>4.320867</td>\n",
              "      <td>3.261973</td>\n",
              "      <td>3.136442</td>\n",
              "      <td>6.484365</td>\n",
              "      <td>...</td>\n",
              "      <td>13.317933</td>\n",
              "      <td>5.846936</td>\n",
              "      <td>13.735932</td>\n",
              "      <td>7.957781</td>\n",
              "      <td>8.866835</td>\n",
              "      <td>3.764473</td>\n",
              "      <td>4.136442</td>\n",
              "      <td>12.889355</td>\n",
              "      <td>3.764473</td>\n",
              "      <td>10.363511</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>52</th>\n",
              "      <td>102</td>\n",
              "      <td>PA-180058</td>\n",
              "      <td>16</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Progressive Disease</td>\n",
              "      <td>7.970761</td>\n",
              "      <td>6.245478</td>\n",
              "      <td>5.378744</td>\n",
              "      <td>2.613209</td>\n",
              "      <td>6.648833</td>\n",
              "      <td>...</td>\n",
              "      <td>13.701600</td>\n",
              "      <td>5.613209</td>\n",
              "      <td>13.113254</td>\n",
              "      <td>8.942333</td>\n",
              "      <td>8.670660</td>\n",
              "      <td>4.198172</td>\n",
              "      <td>4.814843</td>\n",
              "      <td>13.032959</td>\n",
              "      <td>3.461206</td>\n",
              "      <td>10.527295</td>\n",
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              "    <tr>\n",
              "      <th>53</th>\n",
              "      <td>103</td>\n",
              "      <td>PA-190250</td>\n",
              "      <td>41</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Progressive Disease</td>\n",
              "      <td>7.635382</td>\n",
              "      <td>5.987683</td>\n",
              "      <td>3.665755</td>\n",
              "      <td>2.817758</td>\n",
              "      <td>6.645577</td>\n",
              "      <td>...</td>\n",
              "      <td>13.393865</td>\n",
              "      <td>5.955262</td>\n",
              "      <td>13.194318</td>\n",
              "      <td>7.154042</td>\n",
              "      <td>7.995676</td>\n",
              "      <td>3.303185</td>\n",
              "      <td>3.955262</td>\n",
              "      <td>13.242974</td>\n",
              "      <td>3.080793</td>\n",
              "      <td>11.286179</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>54</th>\n",
              "      <td>104</td>\n",
              "      <td>PA-190487</td>\n",
              "      <td>49</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Progressive Disease</td>\n",
              "      <td>7.721606</td>\n",
              "      <td>6.441498</td>\n",
              "      <td>2.716605</td>\n",
              "      <td>2.131643</td>\n",
              "      <td>6.500877</td>\n",
              "      <td>...</td>\n",
              "      <td>12.981830</td>\n",
              "      <td>6.146593</td>\n",
              "      <td>12.718795</td>\n",
              "      <td>8.311552</td>\n",
              "      <td>8.670802</td>\n",
              "      <td>3.453571</td>\n",
              "      <td>4.354035</td>\n",
              "      <td>12.725967</td>\n",
              "      <td>3.938998</td>\n",
              "      <td>10.858429</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>55</th>\n",
              "      <td>105</td>\n",
              "      <td>PA-200870</td>\n",
              "      <td>64</td>\n",
              "      <td>Baseline</td>\n",
              "      <td>Progressive Disease</td>\n",
              "      <td>7.626712</td>\n",
              "      <td>0.359925</td>\n",
              "      <td>4.167280</td>\n",
              "      <td>3.681854</td>\n",
              "      <td>6.734965</td>\n",
              "      <td>...</td>\n",
              "      <td>13.286777</td>\n",
              "      <td>6.786190</td>\n",
              "      <td>13.936528</td>\n",
              "      <td>7.867720</td>\n",
              "      <td>8.192815</td>\n",
              "      <td>4.681854</td>\n",
              "      <td>4.167280</td>\n",
              "      <td>12.713348</td>\n",
              "      <td>4.060365</td>\n",
              "      <td>10.283253</td>\n",
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              "<p>56 rows × 736 columns</p>\n",
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          "metadata": {},
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    },
    {
      "cell_type": "code",
      "source": [
        "# Create a new column 'response_label' with the same values as 'Response'\n",
        "full_dataset['response_label'] = full_dataset['Response']\n",
        "\n",
        "# 0 refers to response to treatment, 1 refers to non_respons to treatment\n",
        "full_dataset.loc[full_dataset['Response'] == 'Disease Control', 'response_label'] = 0\n",
        "full_dataset.loc[full_dataset['Response'] == 'Progressive Disease', 'response_label'] = 1"
      ],
      "metadata": {
        "id": "zqqM8JAGEWf8"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "response_df = pandas.DataFrame(full_dataset['response_label'])\n",
        "response_df"
      ],
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      "execution_count": null,
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              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>10</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>11</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>12</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>13</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>14</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>15</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>16</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>17</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>18</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>19</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>20</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>21</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>22</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>23</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>24</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>25</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>26</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>27</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>28</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>29</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>30</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>31</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>32</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>33</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>34</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>35</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>36</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>37</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>38</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>39</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>40</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>41</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>42</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>43</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>44</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>45</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>46</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>47</th>\n",
              "      <td>0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>48</th>\n",
              "      <td>1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>49</th>\n",
              "      <td>1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>50</th>\n",
              "      <td>1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>51</th>\n",
              "      <td>1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>52</th>\n",
              "      <td>1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>53</th>\n",
              "      <td>1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>54</th>\n",
              "      <td>1</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>55</th>\n",
              "      <td>1</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "</div>\n",
              "      <button class=\"colab-df-convert\" onclick=\"convertToInteractive('df-f938e2be-ea86-42ae-9b96-c8bf85dc17e2')\"\n",
              "              title=\"Convert this dataframe to an interactive table.\"\n",
              "              style=\"display:none;\">\n",
              "        \n",
              "  <svg xmlns=\"http://www.w3.org/2000/svg\" height=\"24px\"viewBox=\"0 0 24 24\"\n",
              "       width=\"24px\">\n",
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              "      \n",
              "  <style>\n",
              "    .colab-df-container {\n",
              "      display:flex;\n",
              "      flex-wrap:wrap;\n",
              "      gap: 12px;\n",
              "    }\n",
              "\n",
              "    .colab-df-convert {\n",
              "      background-color: #E8F0FE;\n",
              "      border: none;\n",
              "      border-radius: 50%;\n",
              "      cursor: pointer;\n",
              "      display: none;\n",
              "      fill: #1967D2;\n",
              "      height: 32px;\n",
              "      padding: 0 0 0 0;\n",
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              "    .colab-df-convert:hover {\n",
              "      background-color: #E2EBFA;\n",
              "      box-shadow: 0px 1px 2px rgba(60, 64, 67, 0.3), 0px 1px 3px 1px rgba(60, 64, 67, 0.15);\n",
              "      fill: #174EA6;\n",
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              "\n",
              "    [theme=dark] .colab-df-convert {\n",
              "      background-color: #3B4455;\n",
              "      fill: #D2E3FC;\n",
              "    }\n",
              "\n",
              "    [theme=dark] .colab-df-convert:hover {\n",
              "      background-color: #434B5C;\n",
              "      box-shadow: 0px 1px 3px 1px rgba(0, 0, 0, 0.15);\n",
              "      filter: drop-shadow(0px 1px 2px rgba(0, 0, 0, 0.3));\n",
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              "          document.querySelector('#df-f938e2be-ea86-42ae-9b96-c8bf85dc17e2 button.colab-df-convert');\n",
              "        buttonEl.style.display =\n",
              "          google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
              "\n",
              "        async function convertToInteractive(key) {\n",
              "          const element = document.querySelector('#df-f938e2be-ea86-42ae-9b96-c8bf85dc17e2');\n",
              "          const dataTable =\n",
              "            await google.colab.kernel.invokeFunction('convertToInteractive',\n",
              "                                                     [key], {});\n",
              "          if (!dataTable) return;\n",
              "\n",
              "          const docLinkHtml = 'Like what you see? Visit the ' +\n",
              "            '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
              "            + ' to learn more about interactive tables.';\n",
              "          element.innerHTML = '';\n",
              "          dataTable['output_type'] = 'display_data';\n",
              "          await google.colab.output.renderOutput(dataTable, element);\n",
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              "  </div>\n",
              "  "
            ]
          },
          "metadata": {},
          "execution_count": 131
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "response_df.to_csv('IknowIT_labels.csv', index=False)"
      ],
      "metadata": {
        "id": "Ko3Okq3cGIag"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "full_dataset = full_dataset.drop(['Unnamed: 0', 'Sample.ID', 'Pair', 'Time', 'Response', 'response_label'], axis=1)"
      ],
      "metadata": {
        "id": "5GbN79JQGaTJ"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "full_dataset = np.log2(full_dataset + 1)"
      ],
      "metadata": {
        "id": "jXJ5FXslTZrA"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "full_dataset"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 1000
        },
        "id": "iin76R-ITfmW",
        "outputId": "87d96941-2df5-441d-aefb-13610c0c807d"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "       IRF5.     ELK1.    C4BPA.       C7.   CASP10.      PBK.    CCL25.  \\\n",
              "0   3.197719  2.878126  2.365695  1.868492  3.053971  2.133719  1.047220   \n",
              "1   3.153356  2.903746  2.088608  2.004453  2.929606  2.124424  2.124424   \n",
              "2   3.163384  2.878444  1.729196  1.937346  2.960549  2.142402  1.988233   \n",
              "3   3.185037  2.919872  3.081665  2.038563  2.945850  2.309280  2.199684   \n",
              "4   3.123119  2.673710  1.952228  1.894416  2.972981  2.324010  2.086861   \n",
              "5   3.167551  2.860926  1.828051  1.828051  2.952407  2.213514  1.350821   \n",
              "6   3.142501  2.837393  1.290915  1.854696  2.942090  2.052162  1.914090   \n",
              "7   3.025253  0.485220  2.072845  1.994494  2.974388  2.380495  1.895972   \n",
              "8   3.159905  2.926943  2.047766  1.827693  2.968241  2.047766  2.213239   \n",
              "9   3.149563  2.685187  2.126812  1.691539  2.922294  2.295159  1.893532   \n",
              "10  3.198194  2.971241  3.107499  1.803057  2.953884  2.093288  2.131811   \n",
              "11  3.080516  2.850760  2.317881  1.732499  2.889569  2.457582  2.215666   \n",
              "12  3.103090  2.918020  3.183916  1.770297  2.854643  2.358241  2.202852   \n",
              "13  3.168762  2.895414  2.311748  2.047806  2.943502  2.099891  2.145441   \n",
              "14  3.261415  2.628598  2.855335  1.907386  3.097382  2.463837  2.248318   \n",
              "15  3.126171  2.890308  2.271822  1.907400  2.937008  2.314324  2.223071   \n",
              "16  3.190859  2.974093  2.136911  2.136911  2.996959  2.220710  1.621179   \n",
              "17  3.085760  2.864901  2.193572  1.639202  2.968861  2.354716  2.099248   \n",
              "18  3.184284  2.902415  2.478569  1.995840  2.888211  2.240451  2.209738   \n",
              "19  3.185533  2.895684  1.826660  2.122509  2.895684  2.184963  2.002372   \n",
              "20  3.119379  2.901645  2.179596  1.819777  2.880324  2.278638  2.080899   \n",
              "21  3.019368  2.819507  2.574373  2.128015  2.865660  2.446034  2.128015   \n",
              "22  3.178482  2.415198  2.690243  1.490757  2.985298  2.338650  2.046942   \n",
              "23  3.103705  2.936278  2.396267  2.108792  2.829210  2.367734  2.038032   \n",
              "24  3.204138  2.766932  1.825198  2.226835  2.956203  2.265014  2.183822   \n",
              "25  3.229111  2.965713  2.125867  1.690261  3.015271  2.125867  2.203409   \n",
              "26  3.126001  2.940077  2.211854  1.951277  2.854343  2.211854  1.951277   \n",
              "27  3.170689  2.806633  2.484899  1.829263  3.070225  2.239850  1.748852   \n",
              "28  3.071043  2.885063  2.455029  1.878093  2.903664  1.931075  2.057040   \n",
              "29  3.190220  2.904537  2.442362  1.586092  2.955543  2.253349  1.802307   \n",
              "30  3.308502  2.867981  2.078072  2.018812  3.140891  2.462558  1.948546   \n",
              "31  3.129782  2.913082  2.183827  1.825204  2.856789  2.260477  2.236798   \n",
              "32  3.200223  2.778995  2.230762  2.326464  2.932140  1.969458  2.191653   \n",
              "33  3.077891  2.939614  3.041484  1.642408  2.844963  2.274432  2.005382   \n",
              "34  3.074474  2.968465  2.025788 -1.037475  2.799691  2.102502  2.025788   \n",
              "35  3.208627  2.905156  2.070496  1.893317  2.977605  2.163634  2.163634   \n",
              "36  3.136971  2.841517  2.185493  1.454949  2.902736  1.798438  2.055371   \n",
              "37  3.183958  2.835390  2.149558  1.910290  2.952464  1.850737  1.850737   \n",
              "38  3.228728  1.275135  2.144116  1.275135  2.900067  1.774087  1.774087   \n",
              "39  3.138291  2.944162  1.825493  1.754612  2.963589  2.208605  2.098031   \n",
              "40  3.158532  2.956396  2.308732  2.127472  2.836348  2.199092  2.037901   \n",
              "41  3.057207  2.859271  2.374648  1.518115  2.848087  1.892260  1.950157   \n",
              "42  3.190685  2.752855  2.399125  1.793886  2.974492  2.118342  2.018791   \n",
              "43  3.183542  2.960800  1.737008  1.857160  2.898813  2.265246  1.857160   \n",
              "44  3.141302  2.895242  1.758902  1.674352  2.784965  2.234604  1.942547   \n",
              "45  3.186477  2.859414  2.180247  1.749485  2.884550  2.204865  1.749485   \n",
              "46  3.100053  2.877271  3.199833  2.145598  2.874137  2.104077  2.057181   \n",
              "47  3.164359  2.805114  2.143261  1.938335  2.778709  2.272809  0.873917   \n",
              "48  3.239223  2.848923  2.287677  1.691810  3.038731  2.173360  1.775372   \n",
              "49  3.177252  2.804016  2.124105  1.630541  3.089002  1.630541  2.281498   \n",
              "50  3.115788  2.850962  1.968513  2.096334  2.867128  2.096334  2.296794   \n",
              "51  3.201108  2.411661  2.091521  2.048390  2.903880  1.943710  1.943710   \n",
              "52  3.165230  2.857081  2.673272  1.853281  2.935240  2.035144  1.954659   \n",
              "53  3.110260  2.804814  2.222111  1.932726  2.934625  2.028849  1.319520   \n",
              "54  3.124594  2.895593  1.893986  1.646920  2.907059  1.951815  1.951815   \n",
              "55  3.108811  0.443528  2.369405  2.227080  2.951395  2.369405  2.059106   \n",
              "\n",
              "       CD1D.     TFRC.     FPR2.  ...    ANXA1.  POU2AF1.     SELL.    LAIR2.  \\\n",
              "0   3.423353  3.630598  3.726651  ...  3.811919  2.621526  3.819525  3.007882   \n",
              "1   3.303431  3.601167  3.685025  ...  3.776803  2.994722  3.820026  3.165912   \n",
              "2   3.336359  3.536485  3.717252  ...  3.792839  2.992639  3.830259  3.166021   \n",
              "3   3.318855  3.565061  3.691737  ...  3.838022  2.840256  3.807385  3.219991   \n",
              "4   3.290748  3.573337  3.750619  ...  3.805084  2.860374  3.829860  3.206453   \n",
              "5   3.367428  3.498521  3.734736  ...  3.831813  2.679999  3.856240  3.075034   \n",
              "6   3.296317  3.593001  3.700251  ...  3.780055  2.807648  3.781813  3.163906   \n",
              "7   3.139009  3.659105  3.795180  ...  3.863593  2.891841  3.872940  3.272306   \n",
              "8   3.315705  3.507750  3.679333  ...  3.864418  2.784408  3.832089  3.099642   \n",
              "9   3.319361  3.552113  3.770179  ...  3.808357  2.718199  3.898872  3.225763   \n",
              "10  3.318917  3.561255  3.699172  ...  3.829053  2.822638  3.820580  3.063799   \n",
              "11  3.266143  3.552342  3.731565  ...  3.800814  2.800514  3.873291  3.059698   \n",
              "12  3.278270  3.599971  3.708464  ...  3.802664  2.718343  3.790184  3.186458   \n",
              "13  3.336179  3.735990  3.744552  ...  3.826271  2.736666  3.896328  3.152127   \n",
              "14  3.366253  3.554192  3.838826  ...  3.851953  2.730925  3.965859  3.150652   \n",
              "15  3.195757  3.747537  3.578796  ...  3.793443  2.675535  3.807251  3.137597   \n",
              "16  3.338450  3.492006  3.710194  ...  3.831645  2.948623  3.836132  3.205707   \n",
              "17  3.302535  3.597536  3.724849  ...  3.790002  2.702048  3.815834  3.102770   \n",
              "18  3.280871  3.490380  3.657069  ...  3.830225  2.899642  3.836057  3.243851   \n",
              "19  3.297905  3.387434  3.634260  ...  3.804816  2.886090  3.836837  3.106556   \n",
              "20  3.251662  3.685234  3.575885  ...  3.798658  2.791311  3.791646  3.136251   \n",
              "21  3.322702  3.674380  3.822819  ...  3.817490  2.735666  3.956357  3.151815   \n",
              "22  3.398960  3.608299  3.765805  ...  3.891226  2.799110  3.919706  3.235374   \n",
              "23  3.210725  3.499564  3.693356  ...  3.818590  2.863299  3.810696  3.074372   \n",
              "24  3.331129  3.601489  3.655343  ...  3.829907  2.753859  3.820557  3.054690   \n",
              "25  3.346200  3.560812  3.675752  ...  3.773606  2.934835  3.807470  3.235264   \n",
              "26  3.326981  3.445750  3.639448  ...  3.808429  2.797974  3.774973  3.180287   \n",
              "27  3.348851  3.470148  3.746693  ...  3.862230  2.610734  3.810305  3.251298   \n",
              "28  3.333449  3.488755  3.695260  ...  3.829386  2.746638  3.807802  3.243014   \n",
              "29  3.365175  3.567162  3.714237  ...  3.798143  2.848795  3.873084  3.156854   \n",
              "30  3.398399  3.493853  3.701102  ...  3.871755  2.844342  3.898649  3.136514   \n",
              "31  3.287286  3.667648  3.687537  ...  3.764403  3.004931  3.812422  3.245367   \n",
              "32  3.329320  3.569802  3.653004  ...  3.803471  3.002837  3.830755  3.156431   \n",
              "33  3.237786  3.432332  3.611382  ...  3.762190  2.949330  3.801335  3.160310   \n",
              "34  3.212852  3.495899  3.654110  ...  3.787062  2.900038  3.822476  3.126040   \n",
              "35  3.355482  3.513075  3.712406  ...  3.778026  2.829282  3.819540  3.253243   \n",
              "36  3.262952  3.537588  3.702563  ...  3.811099  2.871129  3.817410  3.073580   \n",
              "37  3.285708  3.430448  3.661656  ...  3.862552  2.728300  3.839356  3.227688   \n",
              "38  3.340217  3.618756  3.812454  ...  3.804011  2.853511  3.878409  3.109305   \n",
              "39  3.306266  3.568482  3.683108  ...  3.812813  2.905600  3.788782  3.262787   \n",
              "40  3.330321  3.628113  3.570376  ...  3.854046  2.846782  3.766480  3.063844   \n",
              "41  3.253045  3.553972  3.635027  ...  3.756206  2.817630  3.803549  3.232694   \n",
              "42  3.308544  3.595249  3.709058  ...  3.807003  2.822188  3.784937  3.134776   \n",
              "43  3.362838  3.366428  3.519596  ...  3.858640  2.904086  3.750390  3.151308   \n",
              "44  3.245258  3.321269  3.427968  ...  3.844117  2.976038  3.775818  3.190495   \n",
              "45  3.395545  3.373872  3.572783  ...  3.903187  2.989105  3.816391  3.103666   \n",
              "46  3.325839  3.552512  3.658333  ...  3.844874  2.676805  3.881258  3.094276   \n",
              "47  3.259813  3.366121  3.711646  ...  3.849868  2.962468  3.845775  3.062846   \n",
              "48  3.427126  3.510668  3.678309  ...  3.826792  2.698074  3.798931  3.213349   \n",
              "49  3.406548  3.481406  3.687018  ...  3.814432  2.694836  3.854963  3.248790   \n",
              "50  3.313585  3.645236  3.753818  ...  3.797696  2.998003  3.910021  3.019042   \n",
              "51  3.329418  3.364184  3.767895  ...  3.839751  2.775458  3.881266  3.163141   \n",
              "52  3.369942  3.518213  3.720448  ...  3.877901  2.725351  3.818979  3.313584   \n",
              "53  3.352406  3.485170  3.636638  ...  3.847382  2.798105  3.827242  3.027515   \n",
              "54  3.284499  3.675613  3.504210  ...  3.805481  2.837256  3.778082  3.219022   \n",
              "55  3.241529  3.588422  3.863274  ...  3.836609  2.960918  3.900773  3.148563   \n",
              "\n",
              "       CTSW.       C9.     IRGM.     CD74.   MAGEA4.     CD3E.  \n",
              "0   3.346967  2.365695  2.133719  3.791468  2.388594  3.490438  \n",
              "1   3.193634  2.239660  2.435873  3.807516  2.124424  3.543434  \n",
              "2   3.302411  2.172512  2.380872  3.841372  2.073311  3.398008  \n",
              "3   3.377132  2.165710  2.441029  3.825535  2.086058  3.490400  \n",
              "4   3.359486  2.238088  2.406721  3.726994  1.952228  3.546875  \n",
              "5   3.297388  2.213514  2.421675  3.825303  2.048074  3.551193  \n",
              "6   3.256704  2.088883  2.378988  3.752444  1.785271  3.544985  \n",
              "7   3.162595  2.380495  2.456087  3.654446  2.192107  3.409882  \n",
              "8   3.397775  2.238669  2.421437  3.837083  2.305097  3.572160  \n",
              "9   3.323945  2.267527  2.295159  3.769371  2.237391  3.512091  \n",
              "10  3.194388  2.227197  2.506458  3.795547  1.803057  3.615068  \n",
              "11  3.257227  2.184414  2.339136  3.738919  2.150074  3.587365  \n",
              "12  3.403036  2.173376  2.497812  3.772120  2.255142  3.615080  \n",
              "13  3.335812  2.185805  2.421468  3.768309  2.145441  3.504436  \n",
              "14  3.260655  2.557971  2.628598  3.823125  2.485242  3.202284  \n",
              "15  3.358090  2.293761  2.456357  3.766265  2.166166  3.572814  \n",
              "16  3.363253  1.872327  2.287951  3.835668  2.343767  3.594270  \n",
              "17  3.285096  2.193572  2.149540  3.775969  2.040870  3.536523  \n",
              "18  3.537059  2.096933  2.240451  3.880561  2.240451  3.531283  \n",
              "19  3.446295  2.283649  2.323826  3.877867  2.122509  3.639107  \n",
              "20  3.351626  2.256466  2.371314  3.801657  2.299416  3.618304  \n",
              "21  3.314126  2.517224  2.632555  3.677255  2.324404  3.421289  \n",
              "22  3.238744  2.379255  2.359603  3.845022  2.207180  3.504313  \n",
              "23  3.503174  2.262652  2.241333  3.797028  2.319437  3.658933  \n",
              "24  3.408472  2.408465  2.183822  3.846521  2.226835  3.600599  \n",
              "25  3.325036  2.266670  2.539063  3.800876  1.965405  3.543613  \n",
              "26  3.402521  2.154496  2.237308  3.796128  2.046212  3.614762  \n",
              "27  3.330752  2.285545  2.263480  3.795022  2.088819  3.530441  \n",
              "28  3.276400  2.267054  2.395296  3.762569  2.246796  3.598337  \n",
              "29  3.294588  2.226638  2.379616  3.804306  2.278088  3.471989  \n",
              "30  3.295823  2.444884  2.384720  3.797089  2.018812  3.420018  \n",
              "31  3.250221  2.341170  2.446379  3.741005  2.236798  3.533103  \n",
              "32  3.305043  2.477234  2.459739  3.844241  2.230762  3.458115  \n",
              "33  3.318761  2.138150  2.356669  3.779923  2.005382  3.630362  \n",
              "34  3.370232  2.025788  2.547137  3.804610  1.870702  3.646628  \n",
              "35  3.254014  2.418771  2.486048  3.807051  2.297637  3.563638  \n",
              "36  3.307869  2.245334  2.453763  3.809356  1.947459  3.605526  \n",
              "37  3.384982  2.203779  2.345048  3.805723  2.048710  3.589718  \n",
              "38  3.240870  2.386140  2.482884  3.809188  2.144116  3.582622  \n",
              "39  3.262061  2.252982  2.413743  3.813926  1.985252  3.552298  \n",
              "40  3.423774  2.230030  2.408198  3.823236  2.127472  3.633514  \n",
              "41  3.413768  2.045164  2.514037  3.749763  2.045164  3.616681  \n",
              "42  3.385233  2.417366  2.521175  3.778120  1.883570  3.530548  \n",
              "43  3.372023  2.228686  2.415064  3.866294  2.141248  3.635720  \n",
              "44  3.391346  2.101413  2.376224  3.880864  1.988909  3.634061  \n",
              "45  3.316209  2.384151  2.384151  3.909597  2.093992  3.559327  \n",
              "46  3.225814  2.387393  2.596756  3.777679  2.246920  3.568800  \n",
              "47  3.406553  2.306877  2.391677  3.829843  1.890291  3.538537  \n",
              "48  3.390483  2.341166  2.341166  3.828039  2.223790  3.516463  \n",
              "49  3.289003  2.124105  2.405428  3.794059  1.472157  3.456184  \n",
              "50  3.219671  2.376777  2.459066  3.799799  2.096334  3.559082  \n",
              "51  3.302587  2.252317  2.360769  3.795908  2.252317  3.506337  \n",
              "52  3.273614  2.378004  2.539740  3.810747  2.157434  3.526982  \n",
              "53  3.169232  2.105405  2.308961  3.832179  2.028849  3.618964  \n",
              "54  3.273635  2.154963  2.420627  3.778836  2.304218  3.567841  \n",
              "55  3.200507  2.506362  2.369405  3.777509  2.339241  3.496111  \n",
              "\n",
              "[56 rows x 731 columns]"
            ],
            "text/html": [
              "\n",
              "  <div id=\"df-92777ac5-7c65-4458-a103-f22f3f354a78\">\n",
              "    <div class=\"colab-df-container\">\n",
              "      <div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
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              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>IRF5.</th>\n",
              "      <th>ELK1.</th>\n",
              "      <th>C4BPA.</th>\n",
              "      <th>C7.</th>\n",
              "      <th>CASP10.</th>\n",
              "      <th>PBK.</th>\n",
              "      <th>CCL25.</th>\n",
              "      <th>CD1D.</th>\n",
              "      <th>TFRC.</th>\n",
              "      <th>FPR2.</th>\n",
              "      <th>...</th>\n",
              "      <th>ANXA1.</th>\n",
              "      <th>POU2AF1.</th>\n",
              "      <th>SELL.</th>\n",
              "      <th>LAIR2.</th>\n",
              "      <th>CTSW.</th>\n",
              "      <th>C9.</th>\n",
              "      <th>IRGM.</th>\n",
              "      <th>CD74.</th>\n",
              "      <th>MAGEA4.</th>\n",
              "      <th>CD3E.</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>3.197719</td>\n",
              "      <td>2.878126</td>\n",
              "      <td>2.365695</td>\n",
              "      <td>1.868492</td>\n",
              "      <td>3.053971</td>\n",
              "      <td>2.133719</td>\n",
              "      <td>1.047220</td>\n",
              "      <td>3.423353</td>\n",
              "      <td>3.630598</td>\n",
              "      <td>3.726651</td>\n",
              "      <td>...</td>\n",
              "      <td>3.811919</td>\n",
              "      <td>2.621526</td>\n",
              "      <td>3.819525</td>\n",
              "      <td>3.007882</td>\n",
              "      <td>3.346967</td>\n",
              "      <td>2.365695</td>\n",
              "      <td>2.133719</td>\n",
              "      <td>3.791468</td>\n",
              "      <td>2.388594</td>\n",
              "      <td>3.490438</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>3.153356</td>\n",
              "      <td>2.903746</td>\n",
              "      <td>2.088608</td>\n",
              "      <td>2.004453</td>\n",
              "      <td>2.929606</td>\n",
              "      <td>2.124424</td>\n",
              "      <td>2.124424</td>\n",
              "      <td>3.303431</td>\n",
              "      <td>3.601167</td>\n",
              "      <td>3.685025</td>\n",
              "      <td>...</td>\n",
              "      <td>3.776803</td>\n",
              "      <td>2.994722</td>\n",
              "      <td>3.820026</td>\n",
              "      <td>3.165912</td>\n",
              "      <td>3.193634</td>\n",
              "      <td>2.239660</td>\n",
              "      <td>2.435873</td>\n",
              "      <td>3.807516</td>\n",
              "      <td>2.124424</td>\n",
              "      <td>3.543434</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>3.163384</td>\n",
              "      <td>2.878444</td>\n",
              "      <td>1.729196</td>\n",
              "      <td>1.937346</td>\n",
              "      <td>2.960549</td>\n",
              "      <td>2.142402</td>\n",
              "      <td>1.988233</td>\n",
              "      <td>3.336359</td>\n",
              "      <td>3.536485</td>\n",
              "      <td>3.717252</td>\n",
              "      <td>...</td>\n",
              "      <td>3.792839</td>\n",
              "      <td>2.992639</td>\n",
              "      <td>3.830259</td>\n",
              "      <td>3.166021</td>\n",
              "      <td>3.302411</td>\n",
              "      <td>2.172512</td>\n",
              "      <td>2.380872</td>\n",
              "      <td>3.841372</td>\n",
              "      <td>2.073311</td>\n",
              "      <td>3.398008</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>3.185037</td>\n",
              "      <td>2.919872</td>\n",
              "      <td>3.081665</td>\n",
              "      <td>2.038563</td>\n",
              "      <td>2.945850</td>\n",
              "      <td>2.309280</td>\n",
              "      <td>2.199684</td>\n",
              "      <td>3.318855</td>\n",
              "      <td>3.565061</td>\n",
              "      <td>3.691737</td>\n",
              "      <td>...</td>\n",
              "      <td>3.838022</td>\n",
              "      <td>2.840256</td>\n",
              "      <td>3.807385</td>\n",
              "      <td>3.219991</td>\n",
              "      <td>3.377132</td>\n",
              "      <td>2.165710</td>\n",
              "      <td>2.441029</td>\n",
              "      <td>3.825535</td>\n",
              "      <td>2.086058</td>\n",
              "      <td>3.490400</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>3.123119</td>\n",
              "      <td>2.673710</td>\n",
              "      <td>1.952228</td>\n",
              "      <td>1.894416</td>\n",
              "      <td>2.972981</td>\n",
              "      <td>2.324010</td>\n",
              "      <td>2.086861</td>\n",
              "      <td>3.290748</td>\n",
              "      <td>3.573337</td>\n",
              "      <td>3.750619</td>\n",
              "      <td>...</td>\n",
              "      <td>3.805084</td>\n",
              "      <td>2.860374</td>\n",
              "      <td>3.829860</td>\n",
              "      <td>3.206453</td>\n",
              "      <td>3.359486</td>\n",
              "      <td>2.238088</td>\n",
              "      <td>2.406721</td>\n",
              "      <td>3.726994</td>\n",
              "      <td>1.952228</td>\n",
              "      <td>3.546875</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5</th>\n",
              "      <td>3.167551</td>\n",
              "      <td>2.860926</td>\n",
              "      <td>1.828051</td>\n",
              "      <td>1.828051</td>\n",
              "      <td>2.952407</td>\n",
              "      <td>2.213514</td>\n",
              "      <td>1.350821</td>\n",
              "      <td>3.367428</td>\n",
              "      <td>3.498521</td>\n",
              "      <td>3.734736</td>\n",
              "      <td>...</td>\n",
              "      <td>3.831813</td>\n",
              "      <td>2.679999</td>\n",
              "      <td>3.856240</td>\n",
              "      <td>3.075034</td>\n",
              "      <td>3.297388</td>\n",
              "      <td>2.213514</td>\n",
              "      <td>2.421675</td>\n",
              "      <td>3.825303</td>\n",
              "      <td>2.048074</td>\n",
              "      <td>3.551193</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>6</th>\n",
              "      <td>3.142501</td>\n",
              "      <td>2.837393</td>\n",
              "      <td>1.290915</td>\n",
              "      <td>1.854696</td>\n",
              "      <td>2.942090</td>\n",
              "      <td>2.052162</td>\n",
              "      <td>1.914090</td>\n",
              "      <td>3.296317</td>\n",
              "      <td>3.593001</td>\n",
              "      <td>3.700251</td>\n",
              "      <td>...</td>\n",
              "      <td>3.780055</td>\n",
              "      <td>2.807648</td>\n",
              "      <td>3.781813</td>\n",
              "      <td>3.163906</td>\n",
              "      <td>3.256704</td>\n",
              "      <td>2.088883</td>\n",
              "      <td>2.378988</td>\n",
              "      <td>3.752444</td>\n",
              "      <td>1.785271</td>\n",
              "      <td>3.544985</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7</th>\n",
              "      <td>3.025253</td>\n",
              "      <td>0.485220</td>\n",
              "      <td>2.072845</td>\n",
              "      <td>1.994494</td>\n",
              "      <td>2.974388</td>\n",
              "      <td>2.380495</td>\n",
              "      <td>1.895972</td>\n",
              "      <td>3.139009</td>\n",
              "      <td>3.659105</td>\n",
              "      <td>3.795180</td>\n",
              "      <td>...</td>\n",
              "      <td>3.863593</td>\n",
              "      <td>2.891841</td>\n",
              "      <td>3.872940</td>\n",
              "      <td>3.272306</td>\n",
              "      <td>3.162595</td>\n",
              "      <td>2.380495</td>\n",
              "      <td>2.456087</td>\n",
              "      <td>3.654446</td>\n",
              "      <td>2.192107</td>\n",
              "      <td>3.409882</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>8</th>\n",
              "      <td>3.159905</td>\n",
              "      <td>2.926943</td>\n",
              "      <td>2.047766</td>\n",
              "      <td>1.827693</td>\n",
              "      <td>2.968241</td>\n",
              "      <td>2.047766</td>\n",
              "      <td>2.213239</td>\n",
              "      <td>3.315705</td>\n",
              "      <td>3.507750</td>\n",
              "      <td>3.679333</td>\n",
              "      <td>...</td>\n",
              "      <td>3.864418</td>\n",
              "      <td>2.784408</td>\n",
              "      <td>3.832089</td>\n",
              "      <td>3.099642</td>\n",
              "      <td>3.397775</td>\n",
              "      <td>2.238669</td>\n",
              "      <td>2.421437</td>\n",
              "      <td>3.837083</td>\n",
              "      <td>2.305097</td>\n",
              "      <td>3.572160</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>9</th>\n",
              "      <td>3.149563</td>\n",
              "      <td>2.685187</td>\n",
              "      <td>2.126812</td>\n",
              "      <td>1.691539</td>\n",
              "      <td>2.922294</td>\n",
              "      <td>2.295159</td>\n",
              "      <td>1.893532</td>\n",
              "      <td>3.319361</td>\n",
              "      <td>3.552113</td>\n",
              "      <td>3.770179</td>\n",
              "      <td>...</td>\n",
              "      <td>3.808357</td>\n",
              "      <td>2.718199</td>\n",
              "      <td>3.898872</td>\n",
              "      <td>3.225763</td>\n",
              "      <td>3.323945</td>\n",
              "      <td>2.267527</td>\n",
              "      <td>2.295159</td>\n",
              "      <td>3.769371</td>\n",
              "      <td>2.237391</td>\n",
              "      <td>3.512091</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>10</th>\n",
              "      <td>3.198194</td>\n",
              "      <td>2.971241</td>\n",
              "      <td>3.107499</td>\n",
              "      <td>1.803057</td>\n",
              "      <td>2.953884</td>\n",
              "      <td>2.093288</td>\n",
              "      <td>2.131811</td>\n",
              "      <td>3.318917</td>\n",
              "      <td>3.561255</td>\n",
              "      <td>3.699172</td>\n",
              "      <td>...</td>\n",
              "      <td>3.829053</td>\n",
              "      <td>2.822638</td>\n",
              "      <td>3.820580</td>\n",
              "      <td>3.063799</td>\n",
              "      <td>3.194388</td>\n",
              "      <td>2.227197</td>\n",
              "      <td>2.506458</td>\n",
              "      <td>3.795547</td>\n",
              "      <td>1.803057</td>\n",
              "      <td>3.615068</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>11</th>\n",
              "      <td>3.080516</td>\n",
              "      <td>2.850760</td>\n",
              "      <td>2.317881</td>\n",
              "      <td>1.732499</td>\n",
              "      <td>2.889569</td>\n",
              "      <td>2.457582</td>\n",
              "      <td>2.215666</td>\n",
              "      <td>3.266143</td>\n",
              "      <td>3.552342</td>\n",
              "      <td>3.731565</td>\n",
              "      <td>...</td>\n",
              "      <td>3.800814</td>\n",
              "      <td>2.800514</td>\n",
              "      <td>3.873291</td>\n",
              "      <td>3.059698</td>\n",
              "      <td>3.257227</td>\n",
              "      <td>2.184414</td>\n",
              "      <td>2.339136</td>\n",
              "      <td>3.738919</td>\n",
              "      <td>2.150074</td>\n",
              "      <td>3.587365</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>12</th>\n",
              "      <td>3.103090</td>\n",
              "      <td>2.918020</td>\n",
              "      <td>3.183916</td>\n",
              "      <td>1.770297</td>\n",
              "      <td>2.854643</td>\n",
              "      <td>2.358241</td>\n",
              "      <td>2.202852</td>\n",
              "      <td>3.278270</td>\n",
              "      <td>3.599971</td>\n",
              "      <td>3.708464</td>\n",
              "      <td>...</td>\n",
              "      <td>3.802664</td>\n",
              "      <td>2.718343</td>\n",
              "      <td>3.790184</td>\n",
              "      <td>3.186458</td>\n",
              "      <td>3.403036</td>\n",
              "      <td>2.173376</td>\n",
              "      <td>2.497812</td>\n",
              "      <td>3.772120</td>\n",
              "      <td>2.255142</td>\n",
              "      <td>3.615080</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>13</th>\n",
              "      <td>3.168762</td>\n",
              "      <td>2.895414</td>\n",
              "      <td>2.311748</td>\n",
              "      <td>2.047806</td>\n",
              "      <td>2.943502</td>\n",
              "      <td>2.099891</td>\n",
              "      <td>2.145441</td>\n",
              "      <td>3.336179</td>\n",
              "      <td>3.735990</td>\n",
              "      <td>3.744552</td>\n",
              "      <td>...</td>\n",
              "      <td>3.826271</td>\n",
              "      <td>2.736666</td>\n",
              "      <td>3.896328</td>\n",
              "      <td>3.152127</td>\n",
              "      <td>3.335812</td>\n",
              "      <td>2.185805</td>\n",
              "      <td>2.421468</td>\n",
              "      <td>3.768309</td>\n",
              "      <td>2.145441</td>\n",
              "      <td>3.504436</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>14</th>\n",
              "      <td>3.261415</td>\n",
              "      <td>2.628598</td>\n",
              "      <td>2.855335</td>\n",
              "      <td>1.907386</td>\n",
              "      <td>3.097382</td>\n",
              "      <td>2.463837</td>\n",
              "      <td>2.248318</td>\n",
              "      <td>3.366253</td>\n",
              "      <td>3.554192</td>\n",
              "      <td>3.838826</td>\n",
              "      <td>...</td>\n",
              "      <td>3.851953</td>\n",
              "      <td>2.730925</td>\n",
              "      <td>3.965859</td>\n",
              "      <td>3.150652</td>\n",
              "      <td>3.260655</td>\n",
              "      <td>2.557971</td>\n",
              "      <td>2.628598</td>\n",
              "      <td>3.823125</td>\n",
              "      <td>2.485242</td>\n",
              "      <td>3.202284</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>15</th>\n",
              "      <td>3.126171</td>\n",
              "      <td>2.890308</td>\n",
              "      <td>2.271822</td>\n",
              "      <td>1.907400</td>\n",
              "      <td>2.937008</td>\n",
              "      <td>2.314324</td>\n",
              "      <td>2.223071</td>\n",
              "      <td>3.195757</td>\n",
              "      <td>3.747537</td>\n",
              "      <td>3.578796</td>\n",
              "      <td>...</td>\n",
              "      <td>3.793443</td>\n",
              "      <td>2.675535</td>\n",
              "      <td>3.807251</td>\n",
              "      <td>3.137597</td>\n",
              "      <td>3.358090</td>\n",
              "      <td>2.293761</td>\n",
              "      <td>2.456357</td>\n",
              "      <td>3.766265</td>\n",
              "      <td>2.166166</td>\n",
              "      <td>3.572814</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>16</th>\n",
              "      <td>3.190859</td>\n",
              "      <td>2.974093</td>\n",
              "      <td>2.136911</td>\n",
              "      <td>2.136911</td>\n",
              "      <td>2.996959</td>\n",
              "      <td>2.220710</td>\n",
              "      <td>1.621179</td>\n",
              "      <td>3.338450</td>\n",
              "      <td>3.492006</td>\n",
              "      <td>3.710194</td>\n",
              "      <td>...</td>\n",
              "      <td>3.831645</td>\n",
              "      <td>2.948623</td>\n",
              "      <td>3.836132</td>\n",
              "      <td>3.205707</td>\n",
              "      <td>3.363253</td>\n",
              "      <td>1.872327</td>\n",
              "      <td>2.287951</td>\n",
              "      <td>3.835668</td>\n",
              "      <td>2.343767</td>\n",
              "      <td>3.594270</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>17</th>\n",
              "      <td>3.085760</td>\n",
              "      <td>2.864901</td>\n",
              "      <td>2.193572</td>\n",
              "      <td>1.639202</td>\n",
              "      <td>2.968861</td>\n",
              "      <td>2.354716</td>\n",
              "      <td>2.099248</td>\n",
              "      <td>3.302535</td>\n",
              "      <td>3.597536</td>\n",
              "      <td>3.724849</td>\n",
              "      <td>...</td>\n",
              "      <td>3.790002</td>\n",
              "      <td>2.702048</td>\n",
              "      <td>3.815834</td>\n",
              "      <td>3.102770</td>\n",
              "      <td>3.285096</td>\n",
              "      <td>2.193572</td>\n",
              "      <td>2.149540</td>\n",
              "      <td>3.775969</td>\n",
              "      <td>2.040870</td>\n",
              "      <td>3.536523</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>18</th>\n",
              "      <td>3.184284</td>\n",
              "      <td>2.902415</td>\n",
              "      <td>2.478569</td>\n",
              "      <td>1.995840</td>\n",
              "      <td>2.888211</td>\n",
              "      <td>2.240451</td>\n",
              "      <td>2.209738</td>\n",
              "      <td>3.280871</td>\n",
              "      <td>3.490380</td>\n",
              "      <td>3.657069</td>\n",
              "      <td>...</td>\n",
              "      <td>3.830225</td>\n",
              "      <td>2.899642</td>\n",
              "      <td>3.836057</td>\n",
              "      <td>3.243851</td>\n",
              "      <td>3.537059</td>\n",
              "      <td>2.096933</td>\n",
              "      <td>2.240451</td>\n",
              "      <td>3.880561</td>\n",
              "      <td>2.240451</td>\n",
              "      <td>3.531283</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>19</th>\n",
              "      <td>3.185533</td>\n",
              "      <td>2.895684</td>\n",
              "      <td>1.826660</td>\n",
              "      <td>2.122509</td>\n",
              "      <td>2.895684</td>\n",
              "      <td>2.184963</td>\n",
              "      <td>2.002372</td>\n",
              "      <td>3.297905</td>\n",
              "      <td>3.387434</td>\n",
              "      <td>3.634260</td>\n",
              "      <td>...</td>\n",
              "      <td>3.804816</td>\n",
              "      <td>2.886090</td>\n",
              "      <td>3.836837</td>\n",
              "      <td>3.106556</td>\n",
              "      <td>3.446295</td>\n",
              "      <td>2.283649</td>\n",
              "      <td>2.323826</td>\n",
              "      <td>3.877867</td>\n",
              "      <td>2.122509</td>\n",
              "      <td>3.639107</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>20</th>\n",
              "      <td>3.119379</td>\n",
              "      <td>2.901645</td>\n",
              "      <td>2.179596</td>\n",
              "      <td>1.819777</td>\n",
              "      <td>2.880324</td>\n",
              "      <td>2.278638</td>\n",
              "      <td>2.080899</td>\n",
              "      <td>3.251662</td>\n",
              "      <td>3.685234</td>\n",
              "      <td>3.575885</td>\n",
              "      <td>...</td>\n",
              "      <td>3.798658</td>\n",
              "      <td>2.791311</td>\n",
              "      <td>3.791646</td>\n",
              "      <td>3.136251</td>\n",
              "      <td>3.351626</td>\n",
              "      <td>2.256466</td>\n",
              "      <td>2.371314</td>\n",
              "      <td>3.801657</td>\n",
              "      <td>2.299416</td>\n",
              "      <td>3.618304</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>21</th>\n",
              "      <td>3.019368</td>\n",
              "      <td>2.819507</td>\n",
              "      <td>2.574373</td>\n",
              "      <td>2.128015</td>\n",
              "      <td>2.865660</td>\n",
              "      <td>2.446034</td>\n",
              "      <td>2.128015</td>\n",
              "      <td>3.322702</td>\n",
              "      <td>3.674380</td>\n",
              "      <td>3.822819</td>\n",
              "      <td>...</td>\n",
              "      <td>3.817490</td>\n",
              "      <td>2.735666</td>\n",
              "      <td>3.956357</td>\n",
              "      <td>3.151815</td>\n",
              "      <td>3.314126</td>\n",
              "      <td>2.517224</td>\n",
              "      <td>2.632555</td>\n",
              "      <td>3.677255</td>\n",
              "      <td>2.324404</td>\n",
              "      <td>3.421289</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>22</th>\n",
              "      <td>3.178482</td>\n",
              "      <td>2.415198</td>\n",
              "      <td>2.690243</td>\n",
              "      <td>1.490757</td>\n",
              "      <td>2.985298</td>\n",
              "      <td>2.338650</td>\n",
              "      <td>2.046942</td>\n",
              "      <td>3.398960</td>\n",
              "      <td>3.608299</td>\n",
              "      <td>3.765805</td>\n",
              "      <td>...</td>\n",
              "      <td>3.891226</td>\n",
              "      <td>2.799110</td>\n",
              "      <td>3.919706</td>\n",
              "      <td>3.235374</td>\n",
              "      <td>3.238744</td>\n",
              "      <td>2.379255</td>\n",
              "      <td>2.359603</td>\n",
              "      <td>3.845022</td>\n",
              "      <td>2.207180</td>\n",
              "      <td>3.504313</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>23</th>\n",
              "      <td>3.103705</td>\n",
              "      <td>2.936278</td>\n",
              "      <td>2.396267</td>\n",
              "      <td>2.108792</td>\n",
              "      <td>2.829210</td>\n",
              "      <td>2.367734</td>\n",
              "      <td>2.038032</td>\n",
              "      <td>3.210725</td>\n",
              "      <td>3.499564</td>\n",
              "      <td>3.693356</td>\n",
              "      <td>...</td>\n",
              "      <td>3.818590</td>\n",
              "      <td>2.863299</td>\n",
              "      <td>3.810696</td>\n",
              "      <td>3.074372</td>\n",
              "      <td>3.503174</td>\n",
              "      <td>2.262652</td>\n",
              "      <td>2.241333</td>\n",
              "      <td>3.797028</td>\n",
              "      <td>2.319437</td>\n",
              "      <td>3.658933</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>24</th>\n",
              "      <td>3.204138</td>\n",
              "      <td>2.766932</td>\n",
              "      <td>1.825198</td>\n",
              "      <td>2.226835</td>\n",
              "      <td>2.956203</td>\n",
              "      <td>2.265014</td>\n",
              "      <td>2.183822</td>\n",
              "      <td>3.331129</td>\n",
              "      <td>3.601489</td>\n",
              "      <td>3.655343</td>\n",
              "      <td>...</td>\n",
              "      <td>3.829907</td>\n",
              "      <td>2.753859</td>\n",
              "      <td>3.820557</td>\n",
              "      <td>3.054690</td>\n",
              "      <td>3.408472</td>\n",
              "      <td>2.408465</td>\n",
              "      <td>2.183822</td>\n",
              "      <td>3.846521</td>\n",
              "      <td>2.226835</td>\n",
              "      <td>3.600599</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>25</th>\n",
              "      <td>3.229111</td>\n",
              "      <td>2.965713</td>\n",
              "      <td>2.125867</td>\n",
              "      <td>1.690261</td>\n",
              "      <td>3.015271</td>\n",
              "      <td>2.125867</td>\n",
              "      <td>2.203409</td>\n",
              "      <td>3.346200</td>\n",
              "      <td>3.560812</td>\n",
              "      <td>3.675752</td>\n",
              "      <td>...</td>\n",
              "      <td>3.773606</td>\n",
              "      <td>2.934835</td>\n",
              "      <td>3.807470</td>\n",
              "      <td>3.235264</td>\n",
              "      <td>3.325036</td>\n",
              "      <td>2.266670</td>\n",
              "      <td>2.539063</td>\n",
              "      <td>3.800876</td>\n",
              "      <td>1.965405</td>\n",
              "      <td>3.543613</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>26</th>\n",
              "      <td>3.126001</td>\n",
              "      <td>2.940077</td>\n",
              "      <td>2.211854</td>\n",
              "      <td>1.951277</td>\n",
              "      <td>2.854343</td>\n",
              "      <td>2.211854</td>\n",
              "      <td>1.951277</td>\n",
              "      <td>3.326981</td>\n",
              "      <td>3.445750</td>\n",
              "      <td>3.639448</td>\n",
              "      <td>...</td>\n",
              "      <td>3.808429</td>\n",
              "      <td>2.797974</td>\n",
              "      <td>3.774973</td>\n",
              "      <td>3.180287</td>\n",
              "      <td>3.402521</td>\n",
              "      <td>2.154496</td>\n",
              "      <td>2.237308</td>\n",
              "      <td>3.796128</td>\n",
              "      <td>2.046212</td>\n",
              "      <td>3.614762</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>27</th>\n",
              "      <td>3.170689</td>\n",
              "      <td>2.806633</td>\n",
              "      <td>2.484899</td>\n",
              "      <td>1.829263</td>\n",
              "      <td>3.070225</td>\n",
              "      <td>2.239850</td>\n",
              "      <td>1.748852</td>\n",
              "      <td>3.348851</td>\n",
              "      <td>3.470148</td>\n",
              "      <td>3.746693</td>\n",
              "      <td>...</td>\n",
              "      <td>3.862230</td>\n",
              "      <td>2.610734</td>\n",
              "      <td>3.810305</td>\n",
              "      <td>3.251298</td>\n",
              "      <td>3.330752</td>\n",
              "      <td>2.285545</td>\n",
              "      <td>2.263480</td>\n",
              "      <td>3.795022</td>\n",
              "      <td>2.088819</td>\n",
              "      <td>3.530441</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>28</th>\n",
              "      <td>3.071043</td>\n",
              "      <td>2.885063</td>\n",
              "      <td>2.455029</td>\n",
              "      <td>1.878093</td>\n",
              "      <td>2.903664</td>\n",
              "      <td>1.931075</td>\n",
              "      <td>2.057040</td>\n",
              "      <td>3.333449</td>\n",
              "      <td>3.488755</td>\n",
              "      <td>3.695260</td>\n",
              "      <td>...</td>\n",
              "      <td>3.829386</td>\n",
              "      <td>2.746638</td>\n",
              "      <td>3.807802</td>\n",
              "      <td>3.243014</td>\n",
              "      <td>3.276400</td>\n",
              "      <td>2.267054</td>\n",
              "      <td>2.395296</td>\n",
              "      <td>3.762569</td>\n",
              "      <td>2.246796</td>\n",
              "      <td>3.598337</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>29</th>\n",
              "      <td>3.190220</td>\n",
              "      <td>2.904537</td>\n",
              "      <td>2.442362</td>\n",
              "      <td>1.586092</td>\n",
              "      <td>2.955543</td>\n",
              "      <td>2.253349</td>\n",
              "      <td>1.802307</td>\n",
              "      <td>3.365175</td>\n",
              "      <td>3.567162</td>\n",
              "      <td>3.714237</td>\n",
              "      <td>...</td>\n",
              "      <td>3.798143</td>\n",
              "      <td>2.848795</td>\n",
              "      <td>3.873084</td>\n",
              "      <td>3.156854</td>\n",
              "      <td>3.294588</td>\n",
              "      <td>2.226638</td>\n",
              "      <td>2.379616</td>\n",
              "      <td>3.804306</td>\n",
              "      <td>2.278088</td>\n",
              "      <td>3.471989</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>30</th>\n",
              "      <td>3.308502</td>\n",
              "      <td>2.867981</td>\n",
              "      <td>2.078072</td>\n",
              "      <td>2.018812</td>\n",
              "      <td>3.140891</td>\n",
              "      <td>2.462558</td>\n",
              "      <td>1.948546</td>\n",
              "      <td>3.398399</td>\n",
              "      <td>3.493853</td>\n",
              "      <td>3.701102</td>\n",
              "      <td>...</td>\n",
              "      <td>3.871755</td>\n",
              "      <td>2.844342</td>\n",
              "      <td>3.898649</td>\n",
              "      <td>3.136514</td>\n",
              "      <td>3.295823</td>\n",
              "      <td>2.444884</td>\n",
              "      <td>2.384720</td>\n",
              "      <td>3.797089</td>\n",
              "      <td>2.018812</td>\n",
              "      <td>3.420018</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>31</th>\n",
              "      <td>3.129782</td>\n",
              "      <td>2.913082</td>\n",
              "      <td>2.183827</td>\n",
              "      <td>1.825204</td>\n",
              "      <td>2.856789</td>\n",
              "      <td>2.260477</td>\n",
              "      <td>2.236798</td>\n",
              "      <td>3.287286</td>\n",
              "      <td>3.667648</td>\n",
              "      <td>3.687537</td>\n",
              "      <td>...</td>\n",
              "      <td>3.764403</td>\n",
              "      <td>3.004931</td>\n",
              "      <td>3.812422</td>\n",
              "      <td>3.245367</td>\n",
              "      <td>3.250221</td>\n",
              "      <td>2.341170</td>\n",
              "      <td>2.446379</td>\n",
              "      <td>3.741005</td>\n",
              "      <td>2.236798</td>\n",
              "      <td>3.533103</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>32</th>\n",
              "      <td>3.200223</td>\n",
              "      <td>2.778995</td>\n",
              "      <td>2.230762</td>\n",
              "      <td>2.326464</td>\n",
              "      <td>2.932140</td>\n",
              "      <td>1.969458</td>\n",
              "      <td>2.191653</td>\n",
              "      <td>3.329320</td>\n",
              "      <td>3.569802</td>\n",
              "      <td>3.653004</td>\n",
              "      <td>...</td>\n",
              "      <td>3.803471</td>\n",
              "      <td>3.002837</td>\n",
              "      <td>3.830755</td>\n",
              "      <td>3.156431</td>\n",
              "      <td>3.305043</td>\n",
              "      <td>2.477234</td>\n",
              "      <td>2.459739</td>\n",
              "      <td>3.844241</td>\n",
              "      <td>2.230762</td>\n",
              "      <td>3.458115</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>33</th>\n",
              "      <td>3.077891</td>\n",
              "      <td>2.939614</td>\n",
              "      <td>3.041484</td>\n",
              "      <td>1.642408</td>\n",
              "      <td>2.844963</td>\n",
              "      <td>2.274432</td>\n",
              "      <td>2.005382</td>\n",
              "      <td>3.237786</td>\n",
              "      <td>3.432332</td>\n",
              "      <td>3.611382</td>\n",
              "      <td>...</td>\n",
              "      <td>3.762190</td>\n",
              "      <td>2.949330</td>\n",
              "      <td>3.801335</td>\n",
              "      <td>3.160310</td>\n",
              "      <td>3.318761</td>\n",
              "      <td>2.138150</td>\n",
              "      <td>2.356669</td>\n",
              "      <td>3.779923</td>\n",
              "      <td>2.005382</td>\n",
              "      <td>3.630362</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>34</th>\n",
              "      <td>3.074474</td>\n",
              "      <td>2.968465</td>\n",
              "      <td>2.025788</td>\n",
              "      <td>-1.037475</td>\n",
              "      <td>2.799691</td>\n",
              "      <td>2.102502</td>\n",
              "      <td>2.025788</td>\n",
              "      <td>3.212852</td>\n",
              "      <td>3.495899</td>\n",
              "      <td>3.654110</td>\n",
              "      <td>...</td>\n",
              "      <td>3.787062</td>\n",
              "      <td>2.900038</td>\n",
              "      <td>3.822476</td>\n",
              "      <td>3.126040</td>\n",
              "      <td>3.370232</td>\n",
              "      <td>2.025788</td>\n",
              "      <td>2.547137</td>\n",
              "      <td>3.804610</td>\n",
              "      <td>1.870702</td>\n",
              "      <td>3.646628</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>35</th>\n",
              "      <td>3.208627</td>\n",
              "      <td>2.905156</td>\n",
              "      <td>2.070496</td>\n",
              "      <td>1.893317</td>\n",
              "      <td>2.977605</td>\n",
              "      <td>2.163634</td>\n",
              "      <td>2.163634</td>\n",
              "      <td>3.355482</td>\n",
              "      <td>3.513075</td>\n",
              "      <td>3.712406</td>\n",
              "      <td>...</td>\n",
              "      <td>3.778026</td>\n",
              "      <td>2.829282</td>\n",
              "      <td>3.819540</td>\n",
              "      <td>3.253243</td>\n",
              "      <td>3.254014</td>\n",
              "      <td>2.418771</td>\n",
              "      <td>2.486048</td>\n",
              "      <td>3.807051</td>\n",
              "      <td>2.297637</td>\n",
              "      <td>3.563638</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>36</th>\n",
              "      <td>3.136971</td>\n",
              "      <td>2.841517</td>\n",
              "      <td>2.185493</td>\n",
              "      <td>1.454949</td>\n",
              "      <td>2.902736</td>\n",
              "      <td>1.798438</td>\n",
              "      <td>2.055371</td>\n",
              "      <td>3.262952</td>\n",
              "      <td>3.537588</td>\n",
              "      <td>3.702563</td>\n",
              "      <td>...</td>\n",
              "      <td>3.811099</td>\n",
              "      <td>2.871129</td>\n",
              "      <td>3.817410</td>\n",
              "      <td>3.073580</td>\n",
              "      <td>3.307869</td>\n",
              "      <td>2.245334</td>\n",
              "      <td>2.453763</td>\n",
              "      <td>3.809356</td>\n",
              "      <td>1.947459</td>\n",
              "      <td>3.605526</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>37</th>\n",
              "      <td>3.183958</td>\n",
              "      <td>2.835390</td>\n",
              "      <td>2.149558</td>\n",
              "      <td>1.910290</td>\n",
              "      <td>2.952464</td>\n",
              "      <td>1.850737</td>\n",
              "      <td>1.850737</td>\n",
              "      <td>3.285708</td>\n",
              "      <td>3.430448</td>\n",
              "      <td>3.661656</td>\n",
              "      <td>...</td>\n",
              "      <td>3.862552</td>\n",
              "      <td>2.728300</td>\n",
              "      <td>3.839356</td>\n",
              "      <td>3.227688</td>\n",
              "      <td>3.384982</td>\n",
              "      <td>2.203779</td>\n",
              "      <td>2.345048</td>\n",
              "      <td>3.805723</td>\n",
              "      <td>2.048710</td>\n",
              "      <td>3.589718</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>38</th>\n",
              "      <td>3.228728</td>\n",
              "      <td>1.275135</td>\n",
              "      <td>2.144116</td>\n",
              "      <td>1.275135</td>\n",
              "      <td>2.900067</td>\n",
              "      <td>1.774087</td>\n",
              "      <td>1.774087</td>\n",
              "      <td>3.340217</td>\n",
              "      <td>3.618756</td>\n",
              "      <td>3.812454</td>\n",
              "      <td>...</td>\n",
              "      <td>3.804011</td>\n",
              "      <td>2.853511</td>\n",
              "      <td>3.878409</td>\n",
              "      <td>3.109305</td>\n",
              "      <td>3.240870</td>\n",
              "      <td>2.386140</td>\n",
              "      <td>2.482884</td>\n",
              "      <td>3.809188</td>\n",
              "      <td>2.144116</td>\n",
              "      <td>3.582622</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>39</th>\n",
              "      <td>3.138291</td>\n",
              "      <td>2.944162</td>\n",
              "      <td>1.825493</td>\n",
              "      <td>1.754612</td>\n",
              "      <td>2.963589</td>\n",
              "      <td>2.208605</td>\n",
              "      <td>2.098031</td>\n",
              "      <td>3.306266</td>\n",
              "      <td>3.568482</td>\n",
              "      <td>3.683108</td>\n",
              "      <td>...</td>\n",
              "      <td>3.812813</td>\n",
              "      <td>2.905600</td>\n",
              "      <td>3.788782</td>\n",
              "      <td>3.262787</td>\n",
              "      <td>3.262061</td>\n",
              "      <td>2.252982</td>\n",
              "      <td>2.413743</td>\n",
              "      <td>3.813926</td>\n",
              "      <td>1.985252</td>\n",
              "      <td>3.552298</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>40</th>\n",
              "      <td>3.158532</td>\n",
              "      <td>2.956396</td>\n",
              "      <td>2.308732</td>\n",
              "      <td>2.127472</td>\n",
              "      <td>2.836348</td>\n",
              "      <td>2.199092</td>\n",
              "      <td>2.037901</td>\n",
              "      <td>3.330321</td>\n",
              "      <td>3.628113</td>\n",
              "      <td>3.570376</td>\n",
              "      <td>...</td>\n",
              "      <td>3.854046</td>\n",
              "      <td>2.846782</td>\n",
              "      <td>3.766480</td>\n",
              "      <td>3.063844</td>\n",
              "      <td>3.423774</td>\n",
              "      <td>2.230030</td>\n",
              "      <td>2.408198</td>\n",
              "      <td>3.823236</td>\n",
              "      <td>2.127472</td>\n",
              "      <td>3.633514</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>41</th>\n",
              "      <td>3.057207</td>\n",
              "      <td>2.859271</td>\n",
              "      <td>2.374648</td>\n",
              "      <td>1.518115</td>\n",
              "      <td>2.848087</td>\n",
              "      <td>1.892260</td>\n",
              "      <td>1.950157</td>\n",
              "      <td>3.253045</td>\n",
              "      <td>3.553972</td>\n",
              "      <td>3.635027</td>\n",
              "      <td>...</td>\n",
              "      <td>3.756206</td>\n",
              "      <td>2.817630</td>\n",
              "      <td>3.803549</td>\n",
              "      <td>3.232694</td>\n",
              "      <td>3.413768</td>\n",
              "      <td>2.045164</td>\n",
              "      <td>2.514037</td>\n",
              "      <td>3.749763</td>\n",
              "      <td>2.045164</td>\n",
              "      <td>3.616681</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>42</th>\n",
              "      <td>3.190685</td>\n",
              "      <td>2.752855</td>\n",
              "      <td>2.399125</td>\n",
              "      <td>1.793886</td>\n",
              "      <td>2.974492</td>\n",
              "      <td>2.118342</td>\n",
              "      <td>2.018791</td>\n",
              "      <td>3.308544</td>\n",
              "      <td>3.595249</td>\n",
              "      <td>3.709058</td>\n",
              "      <td>...</td>\n",
              "      <td>3.807003</td>\n",
              "      <td>2.822188</td>\n",
              "      <td>3.784937</td>\n",
              "      <td>3.134776</td>\n",
              "      <td>3.385233</td>\n",
              "      <td>2.417366</td>\n",
              "      <td>2.521175</td>\n",
              "      <td>3.778120</td>\n",
              "      <td>1.883570</td>\n",
              "      <td>3.530548</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>43</th>\n",
              "      <td>3.183542</td>\n",
              "      <td>2.960800</td>\n",
              "      <td>1.737008</td>\n",
              "      <td>1.857160</td>\n",
              "      <td>2.898813</td>\n",
              "      <td>2.265246</td>\n",
              "      <td>1.857160</td>\n",
              "      <td>3.362838</td>\n",
              "      <td>3.366428</td>\n",
              "      <td>3.519596</td>\n",
              "      <td>...</td>\n",
              "      <td>3.858640</td>\n",
              "      <td>2.904086</td>\n",
              "      <td>3.750390</td>\n",
              "      <td>3.151308</td>\n",
              "      <td>3.372023</td>\n",
              "      <td>2.228686</td>\n",
              "      <td>2.415064</td>\n",
              "      <td>3.866294</td>\n",
              "      <td>2.141248</td>\n",
              "      <td>3.635720</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>44</th>\n",
              "      <td>3.141302</td>\n",
              "      <td>2.895242</td>\n",
              "      <td>1.758902</td>\n",
              "      <td>1.674352</td>\n",
              "      <td>2.784965</td>\n",
              "      <td>2.234604</td>\n",
              "      <td>1.942547</td>\n",
              "      <td>3.245258</td>\n",
              "      <td>3.321269</td>\n",
              "      <td>3.427968</td>\n",
              "      <td>...</td>\n",
              "      <td>3.844117</td>\n",
              "      <td>2.976038</td>\n",
              "      <td>3.775818</td>\n",
              "      <td>3.190495</td>\n",
              "      <td>3.391346</td>\n",
              "      <td>2.101413</td>\n",
              "      <td>2.376224</td>\n",
              "      <td>3.880864</td>\n",
              "      <td>1.988909</td>\n",
              "      <td>3.634061</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>45</th>\n",
              "      <td>3.186477</td>\n",
              "      <td>2.859414</td>\n",
              "      <td>2.180247</td>\n",
              "      <td>1.749485</td>\n",
              "      <td>2.884550</td>\n",
              "      <td>2.204865</td>\n",
              "      <td>1.749485</td>\n",
              "      <td>3.395545</td>\n",
              "      <td>3.373872</td>\n",
              "      <td>3.572783</td>\n",
              "      <td>...</td>\n",
              "      <td>3.903187</td>\n",
              "      <td>2.989105</td>\n",
              "      <td>3.816391</td>\n",
              "      <td>3.103666</td>\n",
              "      <td>3.316209</td>\n",
              "      <td>2.384151</td>\n",
              "      <td>2.384151</td>\n",
              "      <td>3.909597</td>\n",
              "      <td>2.093992</td>\n",
              "      <td>3.559327</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>46</th>\n",
              "      <td>3.100053</td>\n",
              "      <td>2.877271</td>\n",
              "      <td>3.199833</td>\n",
              "      <td>2.145598</td>\n",
              "      <td>2.874137</td>\n",
              "      <td>2.104077</td>\n",
              "      <td>2.057181</td>\n",
              "      <td>3.325839</td>\n",
              "      <td>3.552512</td>\n",
              "      <td>3.658333</td>\n",
              "      <td>...</td>\n",
              "      <td>3.844874</td>\n",
              "      <td>2.676805</td>\n",
              "      <td>3.881258</td>\n",
              "      <td>3.094276</td>\n",
              "      <td>3.225814</td>\n",
              "      <td>2.387393</td>\n",
              "      <td>2.596756</td>\n",
              "      <td>3.777679</td>\n",
              "      <td>2.246920</td>\n",
              "      <td>3.568800</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>47</th>\n",
              "      <td>3.164359</td>\n",
              "      <td>2.805114</td>\n",
              "      <td>2.143261</td>\n",
              "      <td>1.938335</td>\n",
              "      <td>2.778709</td>\n",
              "      <td>2.272809</td>\n",
              "      <td>0.873917</td>\n",
              "      <td>3.259813</td>\n",
              "      <td>3.366121</td>\n",
              "      <td>3.711646</td>\n",
              "      <td>...</td>\n",
              "      <td>3.849868</td>\n",
              "      <td>2.962468</td>\n",
              "      <td>3.845775</td>\n",
              "      <td>3.062846</td>\n",
              "      <td>3.406553</td>\n",
              "      <td>2.306877</td>\n",
              "      <td>2.391677</td>\n",
              "      <td>3.829843</td>\n",
              "      <td>1.890291</td>\n",
              "      <td>3.538537</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>48</th>\n",
              "      <td>3.239223</td>\n",
              "      <td>2.848923</td>\n",
              "      <td>2.287677</td>\n",
              "      <td>1.691810</td>\n",
              "      <td>3.038731</td>\n",
              "      <td>2.173360</td>\n",
              "      <td>1.775372</td>\n",
              "      <td>3.427126</td>\n",
              "      <td>3.510668</td>\n",
              "      <td>3.678309</td>\n",
              "      <td>...</td>\n",
              "      <td>3.826792</td>\n",
              "      <td>2.698074</td>\n",
              "      <td>3.798931</td>\n",
              "      <td>3.213349</td>\n",
              "      <td>3.390483</td>\n",
              "      <td>2.341166</td>\n",
              "      <td>2.341166</td>\n",
              "      <td>3.828039</td>\n",
              "      <td>2.223790</td>\n",
              "      <td>3.516463</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>49</th>\n",
              "      <td>3.177252</td>\n",
              "      <td>2.804016</td>\n",
              "      <td>2.124105</td>\n",
              "      <td>1.630541</td>\n",
              "      <td>3.089002</td>\n",
              "      <td>1.630541</td>\n",
              "      <td>2.281498</td>\n",
              "      <td>3.406548</td>\n",
              "      <td>3.481406</td>\n",
              "      <td>3.687018</td>\n",
              "      <td>...</td>\n",
              "      <td>3.814432</td>\n",
              "      <td>2.694836</td>\n",
              "      <td>3.854963</td>\n",
              "      <td>3.248790</td>\n",
              "      <td>3.289003</td>\n",
              "      <td>2.124105</td>\n",
              "      <td>2.405428</td>\n",
              "      <td>3.794059</td>\n",
              "      <td>1.472157</td>\n",
              "      <td>3.456184</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>50</th>\n",
              "      <td>3.115788</td>\n",
              "      <td>2.850962</td>\n",
              "      <td>1.968513</td>\n",
              "      <td>2.096334</td>\n",
              "      <td>2.867128</td>\n",
              "      <td>2.096334</td>\n",
              "      <td>2.296794</td>\n",
              "      <td>3.313585</td>\n",
              "      <td>3.645236</td>\n",
              "      <td>3.753818</td>\n",
              "      <td>...</td>\n",
              "      <td>3.797696</td>\n",
              "      <td>2.998003</td>\n",
              "      <td>3.910021</td>\n",
              "      <td>3.019042</td>\n",
              "      <td>3.219671</td>\n",
              "      <td>2.376777</td>\n",
              "      <td>2.459066</td>\n",
              "      <td>3.799799</td>\n",
              "      <td>2.096334</td>\n",
              "      <td>3.559082</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>51</th>\n",
              "      <td>3.201108</td>\n",
              "      <td>2.411661</td>\n",
              "      <td>2.091521</td>\n",
              "      <td>2.048390</td>\n",
              "      <td>2.903880</td>\n",
              "      <td>1.943710</td>\n",
              "      <td>1.943710</td>\n",
              "      <td>3.329418</td>\n",
              "      <td>3.364184</td>\n",
              "      <td>3.767895</td>\n",
              "      <td>...</td>\n",
              "      <td>3.839751</td>\n",
              "      <td>2.775458</td>\n",
              "      <td>3.881266</td>\n",
              "      <td>3.163141</td>\n",
              "      <td>3.302587</td>\n",
              "      <td>2.252317</td>\n",
              "      <td>2.360769</td>\n",
              "      <td>3.795908</td>\n",
              "      <td>2.252317</td>\n",
              "      <td>3.506337</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>52</th>\n",
              "      <td>3.165230</td>\n",
              "      <td>2.857081</td>\n",
              "      <td>2.673272</td>\n",
              "      <td>1.853281</td>\n",
              "      <td>2.935240</td>\n",
              "      <td>2.035144</td>\n",
              "      <td>1.954659</td>\n",
              "      <td>3.369942</td>\n",
              "      <td>3.518213</td>\n",
              "      <td>3.720448</td>\n",
              "      <td>...</td>\n",
              "      <td>3.877901</td>\n",
              "      <td>2.725351</td>\n",
              "      <td>3.818979</td>\n",
              "      <td>3.313584</td>\n",
              "      <td>3.273614</td>\n",
              "      <td>2.378004</td>\n",
              "      <td>2.539740</td>\n",
              "      <td>3.810747</td>\n",
              "      <td>2.157434</td>\n",
              "      <td>3.526982</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>53</th>\n",
              "      <td>3.110260</td>\n",
              "      <td>2.804814</td>\n",
              "      <td>2.222111</td>\n",
              "      <td>1.932726</td>\n",
              "      <td>2.934625</td>\n",
              "      <td>2.028849</td>\n",
              "      <td>1.319520</td>\n",
              "      <td>3.352406</td>\n",
              "      <td>3.485170</td>\n",
              "      <td>3.636638</td>\n",
              "      <td>...</td>\n",
              "      <td>3.847382</td>\n",
              "      <td>2.798105</td>\n",
              "      <td>3.827242</td>\n",
              "      <td>3.027515</td>\n",
              "      <td>3.169232</td>\n",
              "      <td>2.105405</td>\n",
              "      <td>2.308961</td>\n",
              "      <td>3.832179</td>\n",
              "      <td>2.028849</td>\n",
              "      <td>3.618964</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>54</th>\n",
              "      <td>3.124594</td>\n",
              "      <td>2.895593</td>\n",
              "      <td>1.893986</td>\n",
              "      <td>1.646920</td>\n",
              "      <td>2.907059</td>\n",
              "      <td>1.951815</td>\n",
              "      <td>1.951815</td>\n",
              "      <td>3.284499</td>\n",
              "      <td>3.675613</td>\n",
              "      <td>3.504210</td>\n",
              "      <td>...</td>\n",
              "      <td>3.805481</td>\n",
              "      <td>2.837256</td>\n",
              "      <td>3.778082</td>\n",
              "      <td>3.219022</td>\n",
              "      <td>3.273635</td>\n",
              "      <td>2.154963</td>\n",
              "      <td>2.420627</td>\n",
              "      <td>3.778836</td>\n",
              "      <td>2.304218</td>\n",
              "      <td>3.567841</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>55</th>\n",
              "      <td>3.108811</td>\n",
              "      <td>0.443528</td>\n",
              "      <td>2.369405</td>\n",
              "      <td>2.227080</td>\n",
              "      <td>2.951395</td>\n",
              "      <td>2.369405</td>\n",
              "      <td>2.059106</td>\n",
              "      <td>3.241529</td>\n",
              "      <td>3.588422</td>\n",
              "      <td>3.863274</td>\n",
              "      <td>...</td>\n",
              "      <td>3.836609</td>\n",
              "      <td>2.960918</td>\n",
              "      <td>3.900773</td>\n",
              "      <td>3.148563</td>\n",
              "      <td>3.200507</td>\n",
              "      <td>2.506362</td>\n",
              "      <td>2.369405</td>\n",
              "      <td>3.777509</td>\n",
              "      <td>2.339241</td>\n",
              "      <td>3.496111</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>56 rows × 731 columns</p>\n",
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            ]
          },
          "metadata": {},
          "execution_count": 134
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "# import compass to use as training set\n",
        "compass_data1 = pandas.read_csv('preprocessed_tpmRSEMCOMPASS1.csv')"
      ],
      "metadata": {
        "id": "YGYWavrwENJW"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "# remove the endpoint from column names\n",
        "full_dataset.columns = full_dataset.columns.str.replace('.', '')"
      ],
      "metadata": {
        "id": "cqiqDrIaVFP5",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "094a59fa-42d0-4362-b83b-45aa6f9761ca"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stderr",
          "text": [
            "<ipython-input-136-032453943d7d>:2: FutureWarning: The default value of regex will change from True to False in a future version. In addition, single character regular expressions will *not* be treated as literal strings when regex=True.\n",
            "  full_dataset.columns = full_dataset.columns.str.replace('.', '')\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "# for the experiment compass is used as training set and IknowIT as test data so find the overlapping genes\n",
        "common_gene = list(set(full_dataset.columns).intersection(set(compass_data1.columns)))\n",
        "print(len(common_gene))\n",
        "train_compass = compass_data1[list(common_gene)]\n",
        "test_IknowIT = full_dataset[list(common_gene)]"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "2H-S8GkHRmB-",
        "outputId": "7efa42d1-0e85-4fdb-e693-7382b71873f1"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "122\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "test_IknowIT.to_csv('test_IknowIT.csv', index=False)\n",
        "train_compass.to_csv('train_full_compass.csv', index=False)"
      ],
      "metadata": {
        "id": "hreKAcPLVZ2A"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "full_dataset.to_csv('IknowIT_fulldata.csv', index=False)"
      ],
      "metadata": {
        "id": "xRnhR4M-HGwk"
      },
      "execution_count": null,
      "outputs": []
    }
  ],
  "metadata": {
    "colab": {
      "provenance": []
    },
    "kernelspec": {
      "display_name": "Python 3",
      "name": "python3"
    },
    "language_info": {
      "name": "python"
    }
  },
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  "nbformat_minor": 0
}