I have analysed and clustered my single cell rna seq data with methods in the Seurat package. After clustering, I obtained two main clusters: 0 and 1. I used the Seurat SplitDotPlotGG function to visualise the differential expression of a gene of interest X.
SplitDotPlotGG(object, grouping.var = "clusterID", genes.plot = c("geneX"), cols.use = c("blue", "red"), plot.legend = T)
The plot shows clearly that there could be a significant differential expression of geneX between the conditions represented in clusters 0 and 1. However, I cannot see geneX in the list of differentially expressed genes returned when I run:
FindMarkers(object, ident.1 = 0, ident.2 = 1, genes.use = "geneX")
Is there be any explanation for this? Thanks in advance.