5918 Nucleic Acids Research, 2005, Vol. 33, No. 18 Figure 3. Distributions of correlations for the Illumina HumanRef-8 BeadArrays (A) and the Affymetrix HG-U133 Plus 2 arrays (B). Correlations near 1 and 1 reflect probes whose targets are differentially expressed between the two samples. Correlations near zero reflect probes which do not show a dilution effect. The dilution effect is more pronounced for probes targeted at ‘known’ genes. This effect is stronger for Illumina (C) than for Affymetrix (D), though the Illumina platform has fewer probes which cannot be assigned to known genes (Table 1). For complete data see the Supplementary Data. as shown in Figure 3C and D, probes targeted at known (annotated in RefSeq or in the ‘Known Gene’ table of the Golden Path database) genes have a stronger tendency to show a clear dilution effect. This is apparent by the lessening of the central hump in the known genes and its accentuation in the other probes. The effect appears to hold on both platforms, though the Affymetrix platform has many more probes which target other sites in the genome not containing annotated genes (‘unassigned’ probes, Table 1). Despite the overall difference from the ‘known genes’, many of these probe sets do yield strong correlations with the dilution proﬁle, as evidenced by the smaller peaks near 1 and 1, suggesting that they have biologically meaningful targets (Figure 3C and D). The genes that show no or weak dilution effects might sometimes correspond to genes that are not well measured. This is because noise will have a stronger inﬂuence on their measurement, making detecting a dilution effect difﬁcult. Genes that are not expressed at all in either tissue studied will (by deﬁnition) be purely noise. Indeed, as shown in Figure 4, expression level is strongly associated with the mea- surement of a dilution effect on both platforms: many of the probes not showing dilution effects are expressed at lower levels, compared with the probes showing strong effects. As might be expected, there is an interaction of this effect with the known/unassigned gene distinction, and probes with- out known gene assignments tend to show lower expression levels (Supplementary Data). Comparisons between the platforms The key question we wanted to answer was whether these two platforms, measuring the same samples, yield the same results. We therefore identiﬁed probes which map to common genes between the platforms. Based on our own sequence analysis (Table 1 and Materials and Methods), we identiﬁed 28 383 Affymetrix probe sets and 17 711 Illumina probes that could be matched to a common gene (83 and 89% of probes mapped to genes), covering 14 929 known genes altogether. If there was more than one probe(set) for a given gene, when doing comparisons we considered all pos- sible combinations (to avoid repetition, we will use the term ‘probe’ even when we mean Affymetrix ‘probe set’, unless stated explicitly). Thus, if both platforms had two probes for a single gene, there were four comparative values generated. Note that many probes are not speciﬁc for a single transcript of a gene. Probes that could not be matched across platforms