Bossers et al. BMC Genomics 2010, 11:112 http://www.biomedcentral.com/1471-2164/11/112 Page 5 of 13 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. Table 1 The intensity model is favored over the ratio model based on BIC model selection. Cell line dataset Genes Percentage Brain dataset Genes Percentage Ratio 2382 5.49% 4 0.01% Intensity 40976 94.51% 39413 99.99% Total 43358 100.00% 39417 100.00% Results of the per-gene BIC model selection for both the cell line and human brain datasets. The column Ratio represents the number or percentage of genes with lower BIC values as opposed to the intensity model. The Intensity column represents the number or percentage of genes with lower BIC values as opposed to the ratio model. also in this second experimental dataset, there is clear evidence that the intensity model is to be preferred over the ratio model. As the brain dataset is based on human subjects, the biological variation is large, which is reflected in overall less significant p-values than the cell line dataset. Conse- quently, replication on the p-value level is less pro- nounced than for the cell line dataset. We therefore also analyzed replication in the human brain dataset on the treatment effect level. For the two replicate datasets, the size of the treatment effect between different pairwise sample group comparisons (positioned at different dis- tances in the loop design) was estimated using ANOVA models with and without the array factor (Figure 7 and Additional file 5). In all comparisons, the intensity-based