I have citeseq data and I have performed CLR normalization (as used in CITEseq paper)
I see that each Antibody has a different scale (see violin plot). How to compare them?
I generated a dotplot using
sc.pl.dotplot() which takes, according to the function description, values above 0 to consider the fraction of positive cells. I am wondering if this threshold is reliable for citeseq data with CLR transformation.
Thanks a lot for your help.