Distribution of gene-wise correlations between Affymetrix RMA and Illumina. Genes were divided into four groups: genes that were significant (differentially expressed) in both Affymetrix and Illumina (Gai), genes that were significant in Illumina only (Gi), genes that were significant in Affymetrix only (Ga), and genes that were not significant in either platform (Gns). The mean correlations for the four groups were 0.700, 0.358, 0.337, and 0.160, respectively. The variances of the distributions for the four groups were 0.013, 0.060, 0.065, and 0.065, respectively. Using the t-test, Gai is significantly different from Gi and Ga (p < 2.2 × 10-16 for both). Similarly, Gns is significantly different from Gi and Ga (p = 9.463 × 10-16 and < 2.2 × 10-16). The correlations were highest in genes that were significant in both platforms and lowest in genes that were insignificant in both platforms.