MVA and scatter plots. MVA plots (panels A, C, E) and the associated scatter plots (panels B, D, F) for selected technical replicates of Illumina cell line on SAM 1, chosen to demonstrate the nature of biases and variability seen in this study. All axes are on the log base 2 scale where a value of 1.0 corresponds to a 2-fold change. Panels A, C, E: For the MVA plots, the vertical axis is the difference in expression values between the two technical replicates for a given probe and the horizontal axis is the average expression between the two technical replicates. The y = 0 reference line and a loess smoother indicating the average bias as a function of abundance are indicated. The standard deviation of the differences (i.e., of the vertical axis values) is shown for the bottom and top 50% of the data with respect to average abundance as an overall indicator of variation of the plotted points. Panels B, D, F: For the scatter plots, the horizontal axis corresponds to relative expression in the first technical replicate (Rep 1), and the vertical axis the same for the second technical replicate (Rep 2). The y = x reference line and a loess smoother are indicated on the scatter plots, along with the correlation (Spearman's r) as an overall measure of agreement.