Figure 2

The two-stage design in a stringent test situation. (A) Data simulation experiment: empirical density functions of the DE genes (solid curve), noisy non-DE genes (dashed curve), and non-DE genes (dotted curve). The vertical olive lines indicate the simulated FC difference ω between test and control groups. The choice of ω determines the peak of the density function of the DE genes, which lies a little further. The non-DE genes are distributed around a FC difference of 0. A stringent test relative to a FC threshold τ, as indicated by the purple dashed lines, identifies only the DE genes to the right or left of these lines. (B) The positive y axis shows the average number of false discoveries, and the negative y axis shows the average number of missed genes, over 400 generated datasets for three tests relative to a FC threshold. The x axis shows the percentage of DE genes (1%, 10% and 20%) that is simulated in each case. Significance is set at p = 0.01. The data are simulated with respect to a FC difference ω of 1.5. The reference tTREAT with a FC threshold τ of 1.5, thus a test with τ = ω, is depicted in gray and black. The stringent test with a FC threshold τ of 2.5 is in cyan and blue. The decrease (prefixed with a minus sign) or increase (prefixed with a plus sign) in false discoveries or missed genes with respect to the reference (tTREAT with τ of 1.5) is indicated above or below the respective colored bar. When applying tTREAT2 (orange and red) the false discoveries are decreased with regard to the reference test, but the missed genes are not as much increased with regard to the reference test as is the case with the stringent test.