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mnn_correct() ValueError: not enough values to unpack (expected 3, got 1) #757
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Reproducible example: import scanpy as sc
import scanpy.external as ice
from itertools import cycle
pbmc = sc.datasets.pbmc68k_reduced()
sce.pp.mnn_correct(pbmc, batch_key="phase") It looks like As a workaround for now, you could just call |
Thanks, |
@ivirshup Sorry I need to correct my previous answer. Check my issue here chriscainx/mnnpy#27 |
See above and use |
Why is it not maintained? If it doesn’t work, that’s a bug. |
This issue has existed for quite a while now. So I've been using |
Ha, well, it was introduced in #1. Should be easy to fix. |
so "for a while" was accurate 😆 |
Actually this is almost not a bug. The first line of mnn_correct is So we’re just holding it wrong, and it’d work if we passed it a list of anndatas as intended. Why isn’t the API |
fixed in 1611d63 |
Hello,
I am having hard times using the batch correction function running matching mutual nearest neighbors.
I have an anndata with 3 batches. I want to point out that the batch correction using the sc.pp.combat() function works.
On the other hand, if I run (on the uncorrected adata):
I get:
in ..../site-packages/scanpy/preprocessing/_mnn_correct.py the man_correct function is:
I checked _mnn_correct.py. and it basically defines a function mnn_cor on the mnn_correct from mnnpy package:
I think the point is that mnn_cor is not giving 3 values in this line:
Can you pleas help me with that?
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