I have done an analysis in LIMMA to obtain the differential expressed genes. However, now I have 2 questions when I perform GSEA:
Must I order my samples by fold change (first negative and after positive forld change, por example) in a preranked analysis? Is it better to order by p.val? Can I give the list obtained by limma directly in GSEA?
GSEA is usually done with the top genes (let's say, the top 50-100 genes) or must I use THE WHOLE platform (all the 30K probes)?
Thanks in advance