Intra-platform reproducibility of the two microarray platforms. Data on liver sample are shown as a representative example. All 21,171 common genes are represented in these plots. Blue points: concordantly detectable on both replicates; Red points: not detectable in either replicate. (A). M-A plots of two technical replicates analyzed by the two microarray platforms. x-axis: A = 0.5*log2 (Signal_rep1*Signal_rep2); y-axis: M = log2 (Signal_rep1/Signal_rep2). (B). Coefficients of variation (CV) for each microarray platform as a function of gene expression level across four technical replicates. For Agilent arrays, only signals of Cy5 channel were used for illustration in these plots. The black line represents a loess smoothing fitting curve to the 84,684 data points in each platform. (C). Scatter plots of the expression levels measured by each microarray platform for the two technical replicates: For Applied Biosystems arrays, expression levels are represented by signal intensity directly; for Agilent arrays, the expression levels are represented by relative ratio vs. common reference sample (UHR). The black dashed lines indicate the ± 2-fold changes.