Significance of PLINK epistasis p-values

Question

[viavialin]

I performed an epistasis analysis on PLINK using the following options: --epistasis --epi1 1

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.

[bdeonovic]

You should read up on http://en.wikipedia.org/wiki/Multiple_comparisons_problem I would NOT go with the p<0.05 cutoff. Bonferroni correction might be a bit too conservative. Anything significant if you check FDR? If not, you might be out of luck.

[Rm]

try LAMP algorithm or lamplink tool directly;