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

Alan R Dabney1 and John D Storey2*

Author Affiliations

1 Department of Statistics, Texas A&M University, College Station, TX 77843, USA

2 Department of Biostatistics and Department of Genome Sciences, University of Washington, WA 98195, USA

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Genome Biology 2007, 8:R44  doi:10.1186/gb-2007-8-3-r44

Published: 28 March 2007

Abstract

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.