Hello,

I am doing the single cell RNA-seq data analyzing now. I have a treated sample and a non-treated sample. To compare the differences, I have combined these two samples using the official integrating tutorial. My cell populations vary a lot between two samples, so after clustering, in some clusters, there are only very few cells in one sample but lots of cells in other sample.

When I do the Differential expression testing using FindMarkers between these two samples in one cluster, the top genes showed in the results only express in several cells in my many-cell samples, but I want to see the genes specifically broadly expressed in my many-cell samples.

I think the problem is the logic of FindMarkers is: Only the genes expressed in both samples can be compared. But some of my genes may not even emerge in one of my sample. So, are there any way to identify the genes only expressed in one sample in my combined file?

Thank you so much for your help!