Genome Biology
Volume 8
Issue 3 |
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  MethodNormalization of two-channel microarrays accounting for experimental design and intensity-dependent relationshipsAlan R Dabney1  and John D Storey2  1Department of Statistics, Texas A&M University, College Station, TX 77843, USA 2Department of Biostatistics and Department of Genome Sciences, University of Washington, WA 98195, USA  author email corresponding author email
Genome Biology 2007,
8:R44doi:10.1186/gb-2007-8-3-r44
Subject areas: Bioinformatics, Genome studies, Methods 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. | 
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