Normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships. Academic Article uri icon


  • 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.

published proceedings

  • Genome Biol

author list (cited authors)

  • Dabney, A. R., & Storey, J. D.

citation count

  • 21

complete list of authors

  • Dabney, Alan R||Storey, John D

publication date

  • January 2007