Dylan Kotliar

This does seem reasonable. I will accept the pull request. Apologies for not replying sooner.

Hi all, sorry for the bug. @johnjeang - ahh that is very strange, I didn't realize scanpy.pp.normalize_per_cell had that behavior. I can consider changing the default to be min_counts=0. An...

@tianjiaozheng1997 - can you share the command that is causing the error? It looks like there is a formatting error with the input data such that after filtering to only...

Hi @johnjeang - it seems you have some cells with zero counts of the highly variable genes. I believe that in the most current version of the code, the cell...

Hi I think the issue occurs when you have cells that have 0 counts of the high variance genes selected by cNMF. Could you check if this is indeed the...

OK, I finally fixed the bug in the prepare step that was stopping it from printing out the problematic cells that end up with 0 counts of the overdispersed genes....

Hi, I see. Sorry for the slow reply. Can you post the full error trace? My guess is maybe there are cells or genes with 0 counts? Or negative values...

Hi, sorry for slow response @erzakiev. Yes, that is right, we correct the data before cNMF currently. We have developed an approach recently to integrate multiple samples ahead of time...

Thank you!

Hi Han, Yes, exactly, the p-value increased (became less significant). OK thanks for confirming. I found it confusing that even though the association was significant in Cohort2 and pointed in...