I want to do a gene set enrichment analysis. Therefore, in the firest step, I assigned my proteins into COG, NOG categories. But some proteins has multiple COG, NOG categories. Which I thing is normal.
The problem is that I don't know how to handle these proteins in the next step. I think when I will perform the gene set enrichment analysis they will form small groups which in the end will bias the result.
What should I do to avoid this?
Thank for every suggestion.