Using the GoStats package and the org.Mm.eg.db, org.Mm.egGO annotation data I created a list of over represented GO terms for my data set. However, when I attempt to match my genes of interest with the GO terms, the number of genes associated with each GO terms does not perfectly match the "Count" number of genes determined by GoStats. I have tried a variety of methods to over come this issue including:
Using bioMart ensembl data
The AmiGO2 Database
The BioGPS database
Searching within the org.Mm.egGO annotation
but none seem to perfectly match the expected count number. Has anyone else had a similar problem to this and have a solution/ an explanation for why these lists are not matching?