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slot to use for classify_cells function #6

Closed qindan2008 closed 1 year ago

qindan2008 commented 2 years ago

Hi, I wonder which data to use as slot parameter for classify_cells function? In the tirosh_mel80_example, slot ="count", but the count matrix was not integer. So, which slot should be used? "data" or "count"? Thank you!

nttvy commented 2 years ago

Hi @qindan2008

Thank you for having been interested in scAnnotatR. The slot can be either 'data' or 'count' or any other newly created slots, because the expression will then be scaled by genes. The example was actually in normalized data, but we transferred it to 'count' slot to reduce the size of the Seurat object.

Wish my answer helps. Best regards, Vy

qindan2008 commented 2 years ago

OK, thank you very much!

nttvy commented 1 year ago

I guess this issue has been successfully solved, so I close it. Please reopen it if needed.