title: Normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships.
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.
authors: Department of Statistics, Texas A&M University, College Station, TX 77843, USA. adabney@stat.tamu.edu
authors: Alan R
authors: AR
authors: Dabney
authors: John D
authors: JD
authors: Storey
mesh_terms: D046228:Microarray Analysis / Q000592:standards / Q000706:statistics & numerical data*; D015233:Models, Statistical; D012107:Research Design / Q000592:standards* / Q000706:statistics & numerical data