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

Alan R. Dabney, John D. Storey

Research output: Contribution to journalArticlepeer-review

20 Scopus citations

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.

Original languageEnglish (US)
Article numberR44
JournalGenome biology
Volume8
Issue number3
DOIs
StatePublished - Mar 28 2007

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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