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