Hi, I am trying to perform an eQTL analysis using Plink. I consider the gene expression of a particular gene as a quantitative trait and run Plink with the following options --linear --genotypic --mperm 100 --mperm-save-all
According to Plink the first line of the assoc.linear.perm file should contain the stats for the original dataset while the following lines contain stats for permuted phenotypes. When I compare the assoc.linear file that contains p-values and statistics and the first line of the perm file I get different statistics and I don't understand why.
Does somebody know why there is a difference between the stats?
Thanks a lot in advance
I noticed this as well; the P values from association without permutation are from the Wald test (so say the docs). In principle the corresponding values in the permutation result should be the result of the same point-wise test, but in my results they differ slightly.