Hi,
I found DEGs within condition+ cells (the transcript was used during alignment so we are confident these cells are condition+) and across sites. So the DEGs were site 1 vs site 2 within condition+ cells. The cell numbers in the clusters were 9 vs 3, or 10 vs 7, so very few cells, which definitely reduces power. Plus I am using a lot of genes (min.pct=0.25), which significantly impacts FDR correction.
In FindAllMarkers on default (Wilcoxon test), FDR correction does:
> p_adj = (p*Ntests)/rank(p)
So even a raw p-value of 0.05 becomes:
> p_adj = (0.05*15000)/1 = 750 (but is capped at 1)
What should we be doing in this case? Should we just use p_val and treat the genes as exploratory? Are there alternate tests/methods which perform better in sparse cell conditions? Alternate ways to correct for multiple testing?
Appreciate any input!
