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Genome Biol. 2007;8(3):R44.

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

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  • 1Department of Statistics, Texas A&M University, College Station, TX 77843, USA. adabney@stat.tamu.edu


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.

[PubMed - indexed for MEDLINE]
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