Hi there,

I'm trying to do a DEG between groups. I applied these two codes:

Code 1:
marker.genes.cluster <- findMarkers(cdScFiltAnnot_Luminal, groups = cdScFiltAnnot_Luminal$Tissue_Zone, pval.type = "all", BPPARAM = bpp)

Code 2:
marker.genes.cluster.up <- findMarkers(cdScFiltAnnot_Luminal, groups = cdScFiltAnnot_Luminal$Tissue_Zone, pval.type = "all", lfc = 0.5, direction = "up", BPPARAM = bpp)

I'm getting a very different list of upregulated genes for both as below. This is the gene list in descending order of LFC for code 1:

And code 2:

I was wondering if someone can help to explain why I'm getting 2 very different list as I thought the 'direction' and 'lfc' is to help to filter rather than give a very different list. Please help as it will determine which code to use for further downstream analysis.

Thanks