Nanostring data and enrichment analysis
Hi everyone,
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.
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Right, you might have a bias here. I personally think that any enrichment analysis requires a proper set of backgrounds, which typically should be all the genes you analyzed, so the genes included in that panel.
You could use https://biit.cs.ut.ee/gprofiler/gost which accepts custom backgrounds. It also has an R package to call it from inside R.
Thank you ATpoint - I have tried this and unfortunately it did not produce any results despite altering the p-value threshold. Will explore other tools out there.
Perhaps your genes are already so pre-enriched that the number of genes is not sufficient to get the power you need for significant results. Or there is simply no enrichment.