I am using with GWAS data and use the FUMA-online annotation tool for this task. Amongst other things, I am especially interested in mapping eqtls from GTEx to my variants. Here comes my question: FUMA reports for each eqtl the FDR and the p-value.
How would you in general evaluate an eqtl-association: By FDR or by the raw p-value? For some variants the FDR is lower than the p-value and for others the other way around (does this mean sth.?)
I think that FDR makes more sense --> My strategy would be to filter for eqtls with a FDR < 0.05 Does this make sense to you?