Comparison of effect sizes for array and treatment factors. Comparison between the relative sizes of the array and treatment effects, derived from the ANOVA model. Panel A: cell line dataset. Panel B: MAQC dataset. Dashed line: smoothed histogram over all genes for treatment effect size (absolute value of M-value), averaged over all treatment comparisons. Solid line: smoothed histogram over all genes for average array effect size (absolute value of M-value). Note that both the treatment and array effects still include an unavoidable noise component, hence one expects a partial overlap in the histograms because of genes that do not show a differential effect between treatments. Still there is a clear proportion of genes for which the mean treatment effect is much larger than the array effect size.