Any one tried qq-plot for the P-values derived from permutation test in plink (Both EMP1 and EMP2)?
I get a quite strange qq-plot for the pvalues from permutation test to linear regression (phen ~ geno + age)
I also want to know the relationship between EMP1 and EMP2.
EMP1 > EMP2 or EMP1 < EMP2 or they don't have any relationship?
Here, I give a qq-plot for linear regression (phen ~ geno + age)