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How to interpret DEGs found by FindMarkers() with vs without setting latent.vars="donor_ID"?

Open denvercal1234GitHub opened this issue 1 year ago • 0 comments

Hi there,

I performed (A) FindAllMarkers(test.use = "wilcox").

I then ran using the same Seurat object (B) FindAllMarkers(now setting assay = "SCT", only.pos = F, recorrect_umi = FALSE, test.use="MAST", latent.vars="donor_ID").

(B) gave me genes that were not identified by (A). Does it mean these genes are consistently differentially expressed for this cluster across all donors?

I am unclear how I should interpret the difference in the list of returned DEGs using these 2 approaches (paying attention to the confounding effect of donor variability.

Thank you for your help!

denvercal1234GitHub avatar Aug 12 '22 22:08 denvercal1234GitHub