Figure 3. Inter-platform correlation.

A) The absolute expression measurement (brown) and relative expression changes based on gender (grey) were compared between each pair of expression array platforms. The absolute measurement is the average of four samples and the relative change is the difference between two male samples and two female samples. The size of the dots is proportional to platform difference. Data have been processed by quantile-quantile normalization before plotting, so both axes are in the same scale. B) The platform-platform correlation between Affymetrix 3′ array (Mo4302) and gene (MoGene) platforms of absolute expression measurements is dependent on gene expression levels. Average expression measurements were transformed to percentiles. Three blue boxes correspond to low (0 to 10^th percentile), intermediate (45^th to 55^th percentile), and high (90^th to 100^th percentile) transcript abundance as measured by both platforms. Transcript overlap within these three boxes in sequential descending expression order was 48.4%, 24.7%, and 73.2%, respectively.