Finding All Genes (Differential or Not) in Seurat's FindAllMarkers

Question

[bioinformatics2020]

I'm trying to use the marker genes for each cluster generated in Seurat as a pre-ranked list in GSEA. Problem is, I do believe the pre-ranked listed needs to include all genes (those significantly differential and those that are not.) I saw some sample commands on Seurat's Github for doing this, but it did not work for my dataset. Here's what my FindAllMarkers command currently looks like:

sample.markers <- FindAllMarkers(object = sample, only.pos = TRUE, min.pct = 0.25, logfc.threshold = 0.25)

The recommended thresholds on the Github said to put logfc.threshold, min.pct and min.diff.pct all equal to -INF, but this resulted in an empty marker list.

Thanks for the help!

Answer 1

[jared.andrews07]

Try setting them to 0 instead.