Hello,

I am starting using topGO for my GO enrichment analysis and I am running fisher and ks separately. Fisher works fine, but I am not sure about my ks results. My question is: for the ks test, can I use a score different to a p-value? At the moment, I'm working with tajima's D, which generates values between -4 and 4, and my Selected Genes are those with a value higher than 2. So, I want to know if that does not represent any conflict for ks at the moment to run the test.

Thanks  

Theoretically yes, you could use it, you would need to change the selectFun argument, and provide a function that selects the desired genes.

However, I think you won't be able to do it because, what I recall when I tried, the selectFun hadn't changed (it is x < 0.05) and it didn't select any genes.