Nucleic Acids Research, 2005, Vol. 33, No. 18 5919 Figure 4. Distributions of correlations stratified by high and low expression levels (log2) for the Illumina HumanRef-8 BeadArrays (A) and the Affymetrix HG-U133 Plus 2.0 arrays (B). On both platforms, the probes not showing dilution effects tend to express at low levels, whereas highly expressed probes show strong dilution effects. For complete data see the Supplementary Data. Figure 5. Cross-platform agreement for all ‘known’ genes (A), stratified by differential expression (B) and for placenta/blood specific genes (C). For complete data see the Supplementary Data. represent probes which did not map to a ‘known’ gene, or to genes represented on only one platform. A simple hypothesis is that the actual proﬁle of gene expres- sion should agree across platforms for all probes which can be matched to a common gene. As shown in Figure 5A, there is a remarkable level of agreement for many probes by this mea- sure (Pearson correlation was used for this analysis; similar results are obtained with the rank correlation, see Supplemen- tary Data). However, a large population of genes shows poor correlations (peak near zero in Figure 5A). At an FDR of 0.05, 37% of the cross-platform comparisons result in rejection of the hypothesis of no correlation (the threshold correlation to achieve signiﬁcance is 0.56). A more reﬁned analysis takes into account the fact that genes that are not differentially expressed between the two tissues would present noisy expression proﬁles that would not be predicted to be reproducible across platforms. Figure 5B suggests that a large fraction of the ‘failures’ of the platforms to agree can be accounted for by probes which show a weak or no dilution effect. Indeed, if we ﬁrst ﬁlter the data to remove comparisons between probes, of which at least one do not show a signiﬁcant dilution effect (FDR 0.05, removing 48% of the comparisons), rejection of 88% hypotheses yields an FDR of <0.05 (i.e. 88% of the remaining comparisons are signiﬁcant). Using a more stringent Bonferroni correction on this ﬁltered data, 23.7% of the comparisons are considered signiﬁcant at an alpha of 0.05, compared with 8.4% for the unﬁltered data. This enrichment shows that when the dilution effect is considered, the agreement between the platforms rises substantially. A difﬁculty with the analysis shown in Figure 5B and described above is that it relies on the arrays themselves to