Question: TopGO ks test using a score different from p-value
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10 months ago by
eagomezc0
eagomezc0 wrote:

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

modified 10 months ago by Lluís Revilla Sancho470 • written 10 months ago by eagomezc0
Answer: TopGO ks test using a score different from p-value
0
10 months ago by
European Union
Lluís Revilla Sancho470 wrote:

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.