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

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!

scrna-seq deg
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written by khoon0618 • khoon0618

1 answer

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

seuratObject@meta.data$new_condition <- paste0(seuratObject@meta.data$SampleID,"-",seuratObject@meta.data$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.

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written by fracarb8 fracarb8

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

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written by khoon0618 • khoon0618

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