Figure 2

Comparison of SoNG 20 K cDNA array and Lund-zfa array performance. A) Correlation plot comparing hybridization data (for 15,537 gene targets) on the Lund-zfa array (vertical axis) versus the SoNG 20 K array (horizontal axis). Each point shows the mean log2 ratio (male:female) for a single gene. Blue indicates significant difference between males and females (FDR = .05) on both arrays. See Results for discussion of correlation coefficients. B) Principal Components Analysis (PCA) of all data on both array platforms. Each data point represents an array, hybridized to the RNA sample indicated by the adjacent number (1–5 are males and 6–11 are females). The key indicates the array platform. For each gene on each array, expression value was scaled to the overall mean for that gene on that platform. Note that the first principal component (PC1), which explains 16.2 % of the variation, reveals a major effect of sex in the data, independent of platform.