Cross-platform consistency for differential expression analysis. Comparison of cross-platform consistency (U95Av2 versus U133P2), and estimated individual accuracy of differential expression calls using Cleaner (red), AffyProbeMiner (blue) and Affymetrix (black) annotation. Comparisons are made as a function of the z-value threshold used for identifying differentially down-regulated genes (x-axis). (a) Cross-platform consistency was measured as the proportion of genes that are called down-regulated by both platforms to genes that are probed by both platforms and are called down-regulated by at least one of the platforms. (b) Accuracy of individual experiments was measured using FDR estimates from permutation testing, where all probe clusters scoring above threshold in the original data are called true positives and all probe clusters identified in permutated data are called false positives.