Figure 2.

eigenMT Performance

(A) Comparison of empirical p values to adjusted p values from Bonferroni correction (green), eigenMT without regularization (light blue), and eigenMT including regularization (blue). The added regularization prevents anti-conservative results as compared to those from permutations.

(B) Comparison of cis-eQTL discoveries at a FDR of 5% by platform and correction methods.

(C) Effect of sample size on cis-eQTL discovery for the three correction methods. Our method discovers more cis-eQTLs than Bonferroni correction does across all sample sizes.