Smoothed estimates of the quartiles as a function of signal intensity for the p-values and observed t-test statistics for (a, c) dataset 10a and (b, d) dataset 10e. Distributions of the null p-values and test statistics vary with intensity, although less so for the re-loessed datasets (red lines). Even though the medians for the t-statistics seem to be properly centered after re-loessing the data, the quartiles (and hence the variation) are greatly inflated and appear to be intensity dependent. The x-axes show the rankit of the log of the product of the expression means. The y-axes show the observed two-sided p-values (a, b) or the observed t-statistics (c,d). Solid and dashed gray lines indicate the theoretical medians and quartiles, respectively. Black curves correspond to the original datasets and red curves correspond to the re-loessed datasets. Used with permission from .