Example histograms of the sets of P ( d
< 0) values for within and between condition single replicate comparisons – AffyU133A data set. Results shown are for analyses of two arrays from the same experiment (Experiment 3, replicates 1 and 2, left) and two arrays from different experiments (replicate 1 from Experiment 3 and 4, right). Lower panels are blow-ups of the lower part of the upper panels. Notation is as in Figure 4. The histogram on the left exhibits the shape expected under the null-hypothesis of no differentially expressed genes (the grey and black curves overlap), that to the right indicates the presence of small subsets of over- and under-expressed genes.