Figure 6.
Results of GTEx Pilot Study
(A) Manhattan plot of eGene p values from our MVN approach and the permutation test on 3,123 genes in chromosome 1. We performed 10 M samplings with the algorithm for extreme p value approximation for an MVN and 10,000 permutations, which is the commonly used number of permutations in previous studies, for the permutation test.
(B) Plot showing the ratio of MVN eGene p values to permutation-test eGene p values on the 3,123 genes. We performed 1 M permutations for the permutation test and show the ratios for the genes whose corresponding permutation-test eGene p values were greater than 10−4. Blue shading denotes 90% accuracy.
(C) The proportion of genes with error rate < 10% and < 5%. Genes are divided into five bins with the same length, and the proportions are shown for each bin.