Hello, I'm working with a set of RNA-seq data which I want to analyze the Gene Ontolgy Enrichment and the metabolic pathways from Kegg. I have already checked the Pathways and the GO using the hypergeometric test, but I wanted to cross check the results using the Gene Set Enrichment.
Optimally I would like a tool that takes the output of Deseq in some shape and form and runs the GSE test. I have tried GSEA but the results are not what I was expecting (using the metric of -log(pvalue) * sign(logFC)). What tools are currently being used successfully for this kind of analysis?