Accuracy of gene expression measurements by our microarray platform. (A) The measured ratio is compared with the actual ratio, using raw ratio measurements (Raw), ratio after our normalization pipeline (Z-norm), and ratio after MA-LOWESS normalization (MA-norm). Good agreements between measured and actual are observed. The last data point is excluded from the linear regressions. (B) Measurements by microarray are compared with those by RT-PCR in the rat liver experiment. Again a highly linear relationship is observed, with very small compression in the microarray measurements. Our method exhibits a moderate, insignificant improvement over MA-norm. Seven genes with poor quality microarray data (open circles) were excluded from the linear regression.