Topic
Marker gene sanity
Are my cluster markers real cell identity or ribosomal, mitochondrial and stress genes?
FindMarkers returns the genes most different between one cluster and the rest, which is often a dissociation-stress signature, a cell-cycle phase or a sequencing-depth artifact. A marker is only trustworthy if it is specific, expressed in most cells of the cluster, and matches literature you can cite.
- How to Sanity-Check Marker Genes and Cell Type Labels in Spatial Transcriptomics
FindMarkers and rank_genes_groups will happily hand you ribosomal genes and dissociation stress as your top "cell type marker", here is the checklist that catches it before it reaches a figure legend.