MA–scatterplots for direct and reconstructed ratios. Normalized intensity ratios for Kidney vs. Breast comparison from all technical replicates is shown. The yellow dots display the log2 intensity ratio (M) as a function of the log2 intensity product (A) for each gene on the array. Spots that were excluded from further analyses (with intensities below the local background plus 2 SD) are shown in gray. Green lines show the credibility interval thresholds (see Methods) used for estimation of differentially expressed genes.