I'm analyzing some single cell data using Single Cell Experiment package. I'm trying to detect marker genes between clusters using the findMarkers() function. In particular, I wanted to check how many marker genes there are between cluster 3 and 7, which have FDR < 0.01 and a LogFC |1.5|.
When I construct a marker set for cluster 3, the amount of genes with a FDR < 0.01 and a LogFC.7 |2| is 81. But if I construct a marker set for cluster 7, the amount of genes with a FDR < 0.01 and a LogFC.3 |2| is 807.
The thing is that I was expecting to get 81 marker genes with those thresholds also for cluster 7. Since I'm totally new to this topic (and I apologize whether I'm asking a silly question), does anyone know if it's normal to get such a difference between the two clusters? And if yes, could anybody explain me why it's happening?
Thank you in advance