I'm currently trying to run GSEA using a pre-ranked gene list but I'm not sure if my input file is correctly formatted, because my results seem to be mostly insignificant.
So my input looks something like this (roughly 16,000 genes):
Where my ranking statistic is the negative log of the p-Value obtained through an association test.
My results have over 300 gene sets shown to be enriched, but many of them have a FDR p value of close to 1, with a high NES value. What could I be doing wrong?