Hello, I have called histone modification ChIP-seq peaks compared to a control using MACS2 and annotated them using Homer.
I then try to perform pre-ranked GSEA. I only have positive values in my ranking, but I also get negative enrichment so I think GSEA is treating the genes at the bottom of my list as negatively enriched. But they are not; they are just lower but positive. Is there a solution for this? I tried choosing the 'classic' option rather than 'weighted' and it doesn't do it.
Also, what would be the best scoring for pre-ranking? I have fold enrichment, peak score, q-value, p-value and pileup value for each gene.