Performance of the scoring procedure. Comparisons were made between two groups of 2, 3 or 5 replicates. The first group is composed of synthetic data sets made from the experimental replicates Wt-t0a and Wt-t0b, in which 200 genes (100 increased and 100 decreased) are changed with different strengths (p <= 0.30(A), 0.10(B), 0.05(C) or 0.01(D)), and the second group is composed of synthetic data sets without extra variation. Ten comparisons with different combinations of data sets were made, and the resulting mean FDR of increased genes is plotted against given values of S (0.05 to 1, by steps of 0.05). Replicates 2, 3 and 5 are, respectively, plotted with blue interrupted, green dotted, and red continuous lines. Lines marked with circles and without circles refer, respectively, to the results of RDAM and SAM. Only one comparison was used for SAM analysis.