Hello,

I am trying to perform DGE analysis from a CITEseq experiment. I am comparing cells from two groups that I set based on the expression of another cell-surface marker. I have tried to follow FindMarkers() function from Seurat to get a list of DGEs that I then plot in a volcano plot, but I get a weird pattern. My object is log-normalized and follow the default settings from FindMarkers() to use the data assay. I thought FindMarkers assumes data is log1p transformed, so it should not cause a problem.

I am pretty sure there is something else going on, since even as I compare between clusters I get strange logFC values and plots in general.

Thanks!