I am bit confused the use of RNA vs SCT assays for DGE analysis, and wondering if anybody who uses Seurat to shed a light. I've been preforming a Seurat3 integration method with SCTranform by simply following their vignette. According to some discussion and the vignette, a Seurat team indicated that the RNA assay (rather than integrated or Set assays) should be used for DotPlot and FindMarkers functions, for comparing and exploring gene expression differences across cell types. But the RNA assay has raw count data while the SCT assay has scaled and normalized data. It seems to me that numbers in the SCT assay are more appropriate for comparing DGE among cell types. Am I missing something ?