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How to interpret DEGs found by FindMarkers() with vs without setting latent.vars="donor_ID"?
Hi there,
I performed (A) FindAllMarkers(test.use = "wilcox")
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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")
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(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!