Hi,

I have used topGO to create a topGO object and run the enrichment test. So far, so good. Now I want to see which of my selected genes have mapped to the significant GO term. I use:

ann.genes <- genesInTerm(GOdata, sel.terms) ## get the annotations for a significant GO term (ie. sel.terms parameter)

However, none of the genes in the ann.genes is in my initial set of differential/selected genes (that I want to find the enrichment for)! How is this term returned as 'significant', when none of my selected genes belongs to it?

Where am I going wrong? 

thanks!

PS: I'd like to send example data, but it's too large, and i'm not sure how to attach it so that the example is reproducible..

nevermind, got it. My mistake!

thanks!