for associations with multiple comparisons was estimated from p values within each cohort using the R package QVALUE (Storey and Tibshirani, 2003). A π0 value is the overall proportion of true null hypotheses, reflecting the overall behavior of the estimated q-values (alse discovery rates). For example, in our European-American discovery sample, 795 SNPs were tested for associations to derive 795 p values. From these 795 p values, we estimated an overall π0 value to be 0.037 (see Table S28); that is, only 3.7% of these association tests were false positive. In other words, associations between the entire marker set across NKAIN1-SERINC2 region and alcohol dependence in this phenotype group were highly likely (96.3%) to be true positive.
