Hello,
I'm finding it strange to use GO affiliation methodologies based on the list of genes identified in my GWAS windows.
Supposing, my list of genes has about 10 genes per window, and it may be that only one of those genes is actually related to the trait, and the others (9 genes) were listed just because they are close to it. So, in my total list of genes to be considered in clustering analysis, about 90% may not be related to the trait.
This would be different if we were talking about results of RNA-seq, for example. Where all the listed genes were actually expressed differentially.
That said, do you use this type of tool for grouping genes by gene ontology?
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