After trying to read through broad institutes information on analyzing a GSEA plot and piecing together what I could. I still feel like I’m missing something with GSEA plots. Here’s an example I will refer to GSEA
From my understanding you have a gene set of interest which you can then analyze a set of genes against. The GSEA plot will then tell you which genes contribute most to the enrichment score, ie. the genes most enriched by the ontology. You find out which genes are contributing, based upon whether the peak is positive or negative. A positive peak genes to the left of the peak are the main factors, whereas a negative they are to the right?
I guess my biggest questions are how to discern multiple peaks, or in some plots I’ve seen lately two conditions are scored.
If anyone can point me in a more thorough explanation than just the broad institutes, or can provide some help I would greatly appreciate it.