I'm currently learning about Gene Set Enrichment Analysis (GSEA) in the hopes of using it in my analysis of differentially expressed genes, and I just had a few questions about the program, specifically about GSEAPreranked, which I need cleared up.
On the ranked list needed for GSEA input, should the list include all genes, or only those that pass a certain threshold of significance (i.e. fold change higher than 2, p value less than 0.05, etc.)? Ideally I'd like to sort the genes by fold change alone as I don't trust my p values as much, so should I only include genes with high fold changes?
I am comparing multiple conditions of disease with different treatments. Am I correct that GSEA only compares two conditions? If this is the case should I run GSEA for each control/treatment comparison? Would this be conventional?