Figure 3.

(A) Estimates of the fraction π₀ of genes not DE obtained by fitting a quadratic function to the original input (without the flagpole) p-value histogram over the interval [λ, 1]. (B) Density plot of obtained estimates ${\hat{\pi }}_0$. The optimal λ_opt (red dot in (A)) is obtained by choosing the ${\hat{\pi }}_0\left(\lambda \right)$ closest to the mode of the ${\hat{\pi }}_0$ density. The mode is also indicated by the dotted line in (A). The original and corrected p-value histograms are shown in (C) and (D), together with optimally fitted quadratic in (C) and its image after correction in (D). The red part of the quadratic is the interval [λ_opt, 1] in (C) and its image in (D). This example is generated from synthetic data for which the true value of π₀ is 0.85.