gravatar for Papyrus

1 hour ago by

I would use all of the genes that were analyzed in your experiment: these are those on which you performed the differential expression analyses (you maybe previously filtered them to remove low-expression genes, etc.), because (under assumption of independence) those are the ones which had a chance of appearing as DEGs.

Regarding filtering out genes which do not map to GO terms, you can control for this at the GO enrichment step: the goseq function can control this with its use_genes_without_cat argument. And by default (most recent version) these genes are ignored in the enrichment testing.

link

modified 1 hour ago

written
1 hour ago
by

Papyrus180



Source link