I have generated a list of canonical markers for cluster 0 using the following command:
cluster0_canonical <- FindMarkers(project, ident.1=0, ident.2=c(1,2,3,4,5,6,7,8,9,10,11,12,13,14), grouping.var = "status",
min.pct = 0.25, print.bar = FALSE)
And I got the following output, but I do not understand why the canonically expressed ribosomal markers seem to be expressed at high levels in both the cells within the cluster AND cells that are NOT in the cluster (i.e. both pct.1 and pct.2 are close to 1, but P value is highly significant). We would not expect this for canonical markers - we would instead expect the genes to be expressed at high levels in the cells within the cluster but at low levels in cells not within the cluster. I don't seem to have such an issue with non-ribosomal genes within cluster 0 and cluster 0 is the only cluster where I get a high number of ribosomal genes as canonical markers.