plot of zRD of the comparison Exp1D vs Exp1A against zRD of the comparison Exp1C vs Exp1A. Exp1C and Exp1D are synthetic data sets made from the experimental replicates Exp1A and Exp1B (sh100 at t = 0 h). As zRD can be negative, we have plotted positive variations as zRD+2 and negative variations as -zRD-2 to obtain a clear separation of increased and decreased genes. All of the unchanged genes have their zRD set to zero. Red and blue circles mark the genes that received, respectively, an increasing (500 genes) or decreasing (500 genes) additional variation contribution. Black points mark all the genes that did not receive an additional variation contribution. The additional variation p-value was set to 0.30 (A), 0.10 (B), 0.05 (C) and 0.01 (D).