I have a Seurat object of a certain cell type with a UMAP of 7 clusters. I also have information about the sample's origin (primary tumor/metastatic) in my metadata.
Looking at the UMAP I can clearly see that clusters 1 and 5 correspond to metastatic and the other to primary. I wonder if this is the correct way to identify markers genes for those groups:
FindConservedMarkers(nsclc.mac, ident.1 = c(1,5), ident.2 = c(2,3,4,6,7), grouping.var = "stage")