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3.7 years ago
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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.
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.