Issue with topGO output -- Number annotated genes

Question

[javiercalvelo7]

Hello, sorry for the inconvinience but I have a silly question

I'm trying to conduct an anrichment with top GO and I have found an incosistency between the number of annotated genes to be annotated by a given GO term and the number of genes with that GO term actually assigned in the custom annotation file. Near double in some cases. I'm using eggnog mappings and the file seems to be properly formated.

What is the issue? Eggnog doesn't reports the entire hierarchy of GO terms and topGO is recognizing it's child terms?

Thanks

[amelbekkar]

Hello, I am facing the same problem! have you found an answer ? Thanks

[javiercalvelo7]

Actually yes. Eggnog reported the most lower GO terms for each gene and TopGO filled the blanks for the higher GO terms. It is a good beheavior for both tools (saves space) but somehow is not clear in the manual. I ended up checking several genes by hand to be sure.