Figure 2

Sample quantile plots for various sets of null p- values. The x-axes correspond to the expected quantiles for a uniform distribution and the y-axes correspond to the observed (sample) quantiles. (a) Sample quantile plots for the t-test p-values associated with the 152 preprocessing combinations described by [1]. Black lines correspond to the 10 best datasets and are consistent with the curves presented in Figure 1 of [2]. The red lines correspond to re-loessed datasets that were obtained using the same combinations of preprocessing steps as the original 10 sets with the exception that the invariant subsets consisted only of the "present null" (present with fold change = 1) probesets (versus both the "present null" and "empty null" probesets used in [1]). The distribution of the p-values thus depends upon the choice of the invariant subset. (b) Sample quantile curves for dataset 10a. Solid lines correspond to the two-sided p-values and the dashed and dotted lines correspond to the p-values associated with the one sided tests. The model presented in [2] does not account for the discrepancy in the one-sided p-values observed for this dataset, which is not manifest in the re-loessed data (red lines). Similar results are seen with datasets 10b, c, d and 9a, b, c, d. (c) As in (b) but showing sample quantile curves for dataset 10e; dataset 9e is similar. The p-value discrepancies are much less pronounced for these two datasets. This figure appears with permission in the response to [2].