Normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships
Open Access
- 28 March 2007
- journal article
- Published by Springer Nature in Genome Biology
- Vol. 8 (3) , R44
- https://doi.org/10.1186/gb-2007-8-3-r44
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.Keywords
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