I have conducted a search for genetic interactions using a simple dosage model:

Y ~ A + B + AB

where Y is the phenotype, in this case, gene expression values and A and B are vectors of genotype information for ~500 samples. I wish to determine a signficance threshold using permutation testing in order to correct for multiple testing.

To date, I have recalculated the p-values for the interaction term (AB) for 100 permutations (I permuted the phenotype values) and am unsure how to proceed in order to derive a false discovery rate (FDR).

Any suggestions?

Thanks, D.