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Here is a reproducible code for the error:
import scanpy as sc import scanpy.external as ice from itertools import cycle pbmc = sc.datasets.pbmc68k_reduced() pbmc_corrected = mnnpy.mnn_correct(pbmc, batch_key="phase", save_raw=True)
pbmc_corrected
(AnnData object with n_obs × n_vars = 700 × 765 obs: 'bulk_labels', 'n_genes', 'percent_mito', 'n_counts', 'S_score', 'G2M_score', 'phase', 'louvain' var: 'n_counts', 'means', 'dispersions', 'dispersions_norm', 'highly_variable' uns: 'bulk_labels_colors', 'louvain', 'louvain_colors', 'neighbors', 'pca', 'rank_genes_groups' obsm: 'X_pca', 'X_umap' varm: 'PCs',)
type(pbmc_corrected) tuple
type(pbmc_corrected)
tuple
The text was updated successfully, but these errors were encountered:
It expects multiple anndata objects and batch_key is just for concatenating the corrected AnnDatas:
mnnpy/mnnpy/mnn.py
Lines 106 to 107 in 750bba4
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Here is a reproducible code for the error:
pbmc_corrected
type(pbmc_corrected)
tuple
The text was updated successfully, but these errors were encountered: