Bossers et al. BMC Genomics 2010, 11:112 http://www.biomedcentral.com/1471-2164/11/112 Page 8 of 13 Figure 8 Power curves for intensity and ratio models for the MAQC dataset. A-C) Power curves for probes A_32_P215304, A_23_P201338 and A_32_P211558 using treatment effect sizes equal to their estimated values, -0.34, -0.35, -0.50. D) Average power for all probes in the MAQC dataset. Only probes with an estimated effect size larger than 0.25 were taken into account. Solid line: model including array effect; dashed line: model without array effect. reproduced between the two duplicate datasets C1 and C2 when using the intensity analysis, whereas only 73% of the genes is reproduced with the ratio analysis (see Figure 4C). For the brain datasets B1 and B2, the differ- ence between ratio- and intensity-based reproducibility is far more pronounced: only 4% of the top 1,000 genes are reproduced in the ratio analysis, while there is still a substantial overlap of 51% between intensity-based gene rankings (Figure 6C). The underlying reasons behind the apparent discrepancy between the cell line and brain datasets will be addressed later. An independent line of evidence, based on model selection, also indicated that intensity-based models are preferred over ratio-based models for the analysis of dual-color microarray data. When performing Bayesian Information Criterion model selection calculations, we found that for 95% of the transcripts in the cell line experiment, and virtually all transcripts in the human brain experiment, the intensity model was favored over the ratio model. Furthermore, for both the cell line dataset and a publicly available third dataset, a comparison between ANOVA-based array and treatment effect sizes revealed that the treat- ment effects are much larger. Combining the gene ranking, relative effect size and model selection results, we argue that simply by select- ing the intensity model instead of the ratio model for the analysis of the same set of gene expression measure- ments, more reproducible results are obtained. It should be noted that the relative advantage of drop- ping the array effect depends on the complexity of the