How to get DEG considering "clusters" and "samples" at the same time

Question

[khoon0618]

Hello all,

I would like to ask for advice. I am currently analyzing scRNA-seq data from mouse lungs and have finished cluster annotation. However, I am currently struggling to obtain differentially expressed genes (DEGs). It is being analyzed using R's seurat function (seurat object).

Currently, scRNA-seq was performed on the "A" sample and the "B" sample, and as a result, a "Club" cluster and a "Goblet" cluster were obtained. I would like to compare the cellular difference between the "Club" and "Goblet" clusters in sample A with the cellular difference between the Club and Goblet clusters in sample B. A(Club vs Goblet) <> B(Club vs Goblet)

What functions can be used in this case? Thank you very much for your help!

Answer 1

[fracarb8]

You can combine the two conditions and set the Idents to it before running FindMarkers.

[e-mail]$new_condition <- paste0([e-mail]$SampleID,"-",[e-mail]$condition)
Idents(seuratObjec) <- "new_condition"
deg_markers <- FindMarkers(seuratObjec, ident.1 = c("A-Club","A-Goblet"), ident.2 = c("B-Club","B-Goblet"))

I suggest you to define the 2 indents as vectors, so it makes easier to test all the conditions you might have.

[khoon0618]

Thanks for your kind suggestion. I will try with it!