Would greatly appreciate any help regarding how to perform enrichment analysis of DEG from Nanostring (PanCancer Immune Panel). I've used ClueGO however the adjusted P-values (Bonferroni correction) are mostly 1, with the exception of several pathways.
My initial thoughts are, an enrichment analysis using Nanostring sounds counter-intuitive because the reference set of genes itself is already enriched for immune-related pathways. Nevertheless I have seen several papers perform this sort of analysis...
Thank you in advanced.