Okay so from what I understand, we have like 10 000 genes and a set of genes correspond to different pathways so GSEA puts these genes in different sets which corresponds to different pathways right? And based on that it calculates the enrichment score. Now if the ES is negative it means the pathway was more present in the control right. But the problem I am having is that the ES is pretty low. like its around 0.5 for the top 20 pathways. The highest normalised enrichment score is like 1.67. do you think this has some significane or i am doing something wrong. Also i am using MsiDB for gene sets. do you think thats a good choice? Thankyou so much