This one is driving me crazy. I have two data sets, a Vehicle and a Stimulated. These went through the work flow and were integrated as per the the following vignette: Satija lab:Integrating stimulated vs. control PBMC datasets
Everything works great, the data is great. I can find differentially expressed genes for each cluster, irrespective of treatment just fine.
But now I want to find the differentially expressed genes between treatments, within one cluster that I specify. And Im trying to do it in the following way, and I can't figure out why it doesn't work. Everytime the output is the same, no matter what value I enter for subset.ident. Heres an example. My data is in AllCells.combined
Idents(AllCells.combined) <- AllCells.firstname.lastname@example.org$stim DefaultAssay(AllCells.combined) <- "RNA" immune.deg.cluster0 <- FindMarkers(AllCells.combined, ident.1 = "VEH", ident.2 = "IMQ", verbose = TRUE, subset.ident = "0" logfc.threshold = log(2))
This code works for cluster 0 (at least I think its cluster 0) But if i change subset.ident to 1, which I would want to think it would point to cluster 1, it gives me the exact same values as if I had subset 0
I tried using the group.by argument also to no avail.