Bossers et al. BMC Genomics 2010, 11:112 http://www.biomedcentral.com/1471-2164/11/112 Page 6 of 13 Figure 5 Single channel clustering of human brain dataset. Hierarchical clustering of log2-transformed single channel intensities of the human brain experiment. Only genes with an average intensity A > 7 were used. Note that, for all 49 individuals, the two replicate measurements cluster together. Figure 6 Comparison between ratio and intensity model-based reproducibility in the brain dataset. A, B) Comparison between the reproducibility of p-values between the split brain datasets B1 and B2, generated by the ratio model (A) and the intensity model (B). Note the absence of correlation between p-values calculated with the ratio model. p-values are given as -log10(p-value): higher p-values are more significant. C) proportion of genes reproduced in sets of equally ranked genes between the replicate datasets.