Basic questions about GSEA 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?
You seem to refer to the GSEA provided by the Broad institute, (there are other GSEA algorithms). 

1) You can provide whatever you wish, but if you want to know if those gene sets in which side of the ordered list are they, then provide all the list (of genes) you have.

2) GSEA analyize if the order of a given list distributes in certain way the elements of another (unordered) list. In your case you would need to compute the GSEA for each treatment vs control comparison.