Question: Differentially expressed genes between Seurat objects
0
gravatar for lic4010
3 months ago by
lic40100
lic40100 wrote:

Hi all,

I'm trying to find differentially expressed genes between two different subsets of a Seurat object. Is there a straightforward way to do this using FindMarkers() or FindVariableFeatures()? The subsets are pre- and post-treatment and my goal is to find and remove the genes that are associated with the treatment.

thanks!!

ADD COMMENTlink modified 3 months ago by jared.andrews078.3k • written 3 months ago by lic40100

Do you have biological replicates? I am personally a fan of pseudbulk DE for single-cell data. In my hands this denoises the issues related to sparse data quite a lot when it comes to DE testing.

ADD REPLYlink written 3 months ago by ATpoint44k
1
gravatar for jared.andrews07
3 months ago by
jared.andrews078.3k
Memphis, TN
jared.andrews078.3k wrote:

Keep the samples in the same Seurat object, use a model-based test, and include the condition as a latent variable in FindMarkers, i.e. test.use = "LR", latent.vars = "treatment".

ADD COMMENTlink written 3 months ago by jared.andrews078.3k
1

I just want to add that you should use the counts from the RNA assay instead of other assays like SCT or integrated.

ADD REPLYlink written 3 months ago by rpolicastro3.2k
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