Hello, I am trying to find the most highly expressed genes that are conserved in all my scRNAseq clusters with Seurat.
Here is what I tried to do:
YSa.markers <- FindMarkers(object = YSa, ident.1 = 0, ident.2 = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14), min.pct = 0.8) print (x = head(x = YSa.markers, n = 10))
Where 0 to 14 are my clusters.
But when I make Violin plots of the genes that it gives me it’s obvious they are not expressed in all the clusters. I am clearly doing something wrong and I was wondering if anyone could help me with this.
Thank you very much for your time, Michela