Hello everyone,

I would like to ask, after running FindAllMarkers, I obtained about 20 cell clusters. However, I noticed that one of my clusters contains markers for both fibroblasts and T cells. Could this indicate that there is an error in the parameters I set for FindAllMarkers?

The code I use:

data.markers <- FindAllMarkers(combine_datalist, only.pos = TRUE, test.use = "MAST", min.pct = 0.25, logfc.threshold = 0.1)

For example my cluster with mixed cell marker:

EIF4B-Monocytes
MMP3-Fibroblasts
NEAT1-Fibroblasts
TNFAIP6-Fibroblasts
AKR1C1-Fibroblasts
TM4SF1-Fibroblasts
DST-Fibroblasts
CEBPD-Monocytes
MEDAG-Monocytes
EIF1B-Monocytes

What I learned is that normally we only check the top 5 or top 10 markers. However, I want to learn how to deal with this type of situation. Since I will subcluster all my cell types, what if the top expressed or top 3 expressed genes do not correspond to the expected cluster? How should I deal with this situation then?

Thanks for help.