how to find a threshold p value for eqtl analysis

Question

[evafinegan]

Hello,

I am doing eqtl analysis using matrixeqtl package in R. I am using a pvalue of 0.05 in the analysis. But I was wondering if I should use a different threshold pvalue? If so, is there a way to calculate an appropriate threshold pvalue? Thank you for the help!

Answer 1

[Zhenyu Zhang]

normally ppl calculated empirical p-values with permutations.