I'm currently doing analysis on a gene expression dataset produced with the nanostring ncounter method, on a panel of around 700 genes (all involved in the immune system)
I want to test for gene set enrichment, based on the differential expression analysis I've performed between two conditions.
With RNAseq data I usually use the GSEA tool, would it be relevant to also use this tool with a "small" panel of 700 genes? Wouldn't it be biased, as all of those genes are all involved in the immune system?
(I think not but I'm not that sure)
Thank for any of your input !