Normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships

In normalizing two-channel expression arrays, the ANOVA approach explicity incorporates the experimental design in its model, and the MA-plot based approach accounts for intensivity-dependent biases. However, both approaches can lead to inacurate normalization in fairly common scenarios. We propose a method called eCADS for normalizing two-channel microarrays that accounts for both experimental design and intensity-dependent biases. Under reasonable experimental designs, eCADS preserves differential expression relationships and requires only a single array per sample pair.