A and B display the histogram of p-values based on the regularized test statistics from limma or Cyber-T respectively when comparing MNs with dCINs. Horizontal dashed line corresponds to the uniform distribution of p-values under the null hypothesis of no differential expression. A. Mixed model fit to Cyber-T p-values, one beta distribution (red): (λ_{0}, λ_{1}, r, s) = (0.904, 0.0960, 0.206, 1.570). Regressions that included two or three beta-functions gave λ_{2} = λ_{3} = 0. B. Mixed model fit to limma p-values, one beta distribution (red): (λ_{0}, λ_{1}, r, s) = (0.848, 0.152, 0.296, 1.636) and two beta distributions (green): (λ_{0}, λ_{1}, λ_{2}, r_{1}, s_{1}, r_{2}, s_{2}) = (0.760, 0.117, 0.122, 0.265, 2.245, 3.900, 10.042). C. Log transformed p-values versus the FDR for limma (black) and Cyber-T (red) for two different measures of FDR. Plot symbols: +represents mixture model FDR based on the fit to one beta distribution parameters from A or B and closed circles are BH FDR. D. Empirical FDR from SAM as a function of its t-statistic (d-score). Horizontal dashed line in C and D correspond to a 10% FDR cutoff.

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