Hi! I have a data set comprised of microarray results from whole blood, collected from a small group of patients before an intervention (called "baseline") and at several time points after the intervention. The changes are very subtle and so I want to input the data for ALL of the genes (not just DEGs, or those above a certain fold change cut off) and see if any pathways are enriched at later time points compared to baseline, using GSEA and basically a two-class comparison.

I am an immunologist and do not understand the statistics -- is this ok to do? If not, how can I do a similar analysis?

(To be honest, I've already run these analyses using gene expression levels... The results make sense from an immunologist standpoint, but I need to be sure that I'm using the correct statistical methods!)

Thanks!