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saezlab / liana-py

LIANA+: an all-in-one framework for cell-cell communication
http://liana-py.readthedocs.io/
GNU General Public License v3.0
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GeneA_GeneB gene expression level error #115

Open alecdavi opened 4 weeks ago

alecdavi commented 4 weeks ago

Hello,

Thank you really much for this package, it is extremely useful and pleasant to use. I seem to be experiencing an issue when running li.mt.rankaggregate on a single cell sample. Both Gene_A and Gene-B are not expressed in a specific cell type, but I get strong scores for the LR pair Gene_C -> Gene_A_Gene_B. I am not sure where the Gene_A_Gene_B expression comes from and what causes this. Maybe you would have an idea ?

dbdimitrov commented 4 weeks ago

Hi @alecdavi,

Is it possible to share a subset of your data? Or at least the code that you're running?

Thanks!

Daniel

dbdimitrov commented 3 weeks ago

PS. I assume you might be using the .raw of your data, instead of the X