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

2007; BioMed Central; Volume: 8; Issue: 3 Linguagem: Inglês

10.1186/gb-2007-8-3-r44

1474-760X

Alan R. Dabney, John D. Storey,

Gene Regulatory Network Analysis

In normalizing two-channel expression arrays, the ANOVA approach explicitly incorporates the experimental design in its model, and the MA plot-based approach accounts for intensity-dependent biases. However, both approaches can lead to inaccurate normalization in fairly common scenarios. We propose a method called efficient Common Array Dye Swap (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.