Q values used for multiple testing corrections are based on false-discovery rates [30] and were corrected for genomic inflation of significance (Text S1). In addition, permutations (pperm-WY) and Bonferroni adjustment were used for comparison of correction strategies. Permutation p values were obtained by shuffling the endophenotype, while maintaining the covariate structure, 10,000 times and applying the Westfall and Young [60] resampling-style stepdown approach to account for correlations between probes.
