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Batch correction incorrectly assigns cell labels #86
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Hrovatin
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Batch correction incorrectly mixes cell labels
Batch correction incorrectly assigns cell labels
Oct 1, 2023
Hi Karin Thanks for pointing this out, could you kindly add that as a PR we can merge it then |
Btw see here you can do the same thing with cpa: https://cpa-tools.readthedocs.io/en/latest/tutorials/Batch_correction_in_expression_space.html |
Hrovatin
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Oct 1, 2023
The PR is here: #87 |
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I have tried to integrate some of my own data and then reproduce the example from https://scgen.readthedocs.io/en/stable/tutorials/scgen_batch_removal.html , but it seems that the latent data and the obs are not joined correctly, creating wrong cell latent embedding-label pairs.
This is the result from the tutorial, with a clear mismatch between cell type clusters and cell labels
I think the reason could be in https://github.com/theislab/scgen/blob/06084773e56cad0dec340138441dee47a39af752/scgen/_scgen.py#L315C16-L315C16 as you don't check that indices match, but I haven't tested it so it may be a different reason.
scGEN version: 2.1.1
ps. the tutorial also has other mistakes, like cell_type->celltype and the use_rep is missing in neighbours computation for latent
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