I performed an epistasis analysis on PLINK using the following options-
The output from PLINK reports tests significant at a p-value (asymptotic p-value) <1e-4 by default. Since I am not performing a GWAS and I only have 400 SNPs, I changed the output to include all tests.
Do I therefore consider all interaction tests smaller than p<1e-4 as significant or stick to the 'usual' p<0.05?
I performed a Bonferroni correction and nothing was significant. Therefore I am confused on how to interpret the PLINK output p-values.