Figure 4

Intensity models provide more reproducible results than ratio models. A, B) Comparison between the reproducibility of p-values between technically duplicated experiments, generated by the ratio model (A) and the intensity model (B). Note the higher correlation for the intensity model. p-values are given as -log10(p-value): higher p-values are more significant. C) proportion of genes reproduced by either the ratio on intensity model, for sets of equally ranked genes between the replicate datasets C1 and C2.