Dear BioStars Community,
Wondered if anyone could offer some advice on GGProfiler2 and a question about background control for when I use it to do a gene set enrichment analysis (background referring to a gene list for comparison, I believe). Two of the options when using this package include to use "annotated" genes, which are "genes with at least one annotation." In contrast, the other option is "known", which is a list of all the known genes in the organism (see https://rdrr.io/cran/gprofiler2/f/vignettes/gprofiler2.Rmd).
When I compare my experimental gene list with "known" as background I get many more results with ggprofiler2 (which has functions for gene ontology, TRANSFAC analysis etc.), but when I use "annotated" I receive very little or no results. My inclination is to use "known", but I'm not sure if this is reliable or there are other considerations I should be having before just going with this.
Does anyone have any advice on or experience of this?
I really appreciate any advice or help people can offer - thanks!