Figure 1.
Distribution of P-values from tests for differential expression for the two data sets.
P-values were computed from the original data using two sample pooled variance t-tests.
Figure 2.
Distribution of P-values for the two plasmode null data sets.
P-values were computed from two sample pooled variance t-tests.
Table 1.
Quantities of interest in microarray experiments.
Table 2.
Fifteen methods with the source of the software used herein.
Figure 3.
Boxplots for estimates of π0 from 100 plasmodes based on data set 2 for the 15 methods.
Two cases are shown representing A. π0 = 0.8 and B. π0 = 0.9, represented by the horizontal line in the two plots A and B, respectively.
Figure 4.
Plots of estimated FDR (A and C) and LFDR (B and D) using the 15 methods in 100 plasmodes from data set 2 for the case where π0 = 0.9.
Estimates calculated at two thresholds τ = 0.01 (A and B) and 0.001 (C and D) are shown. For the plots of FDR estimates, the horizontal line is the mean of the 100 true values of FDR in the plasmodes and the horizontal dashed lines are the minimum and maximum. True values of LFDR are not known.