title: Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood.
abstract: BACKGROUND
  In two-color microarray experiments, well-known differences exist in the labeling and hybridization efficiency of Cy3 and Cy5 dyes. Previous reports have revealed that these differences can vary on a gene-by-gene basis, an effect termed gene-specific dye bias. If uncorrected, this bias can influence the determination of differentially expressed genes.
  
  
  RESULTS
  We show that the magnitude of the bias scales multiplicatively with signal intensity and is dependent on which nucleotide has been conjugated to the fluorescent dye. A method is proposed to account for gene-specific dye bias within a maximum-likelihood error modeling framework. Using two different labeling schemes, we show that correcting for gene-specific dye bias results in the superior identification of differentially expressed genes within this framework. Improvement is also possible in related ANOVA approaches.
  
  
  BACKGROUND
  A software implementation of this procedure is freely available at http://cellcircuits.org/VERA
authors.affiliation: Program in Bioinformatics and Department of Bioengineering, University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093-0412, USA. rmkelley@ucsd.edu
authors.forename: Ryan
authors.initials: R
authors.lastname: Kelley
authors.forename: Hoda
authors.initials: H
authors.lastname: Feizi
authors.forename: Trey
authors.initials: T
authors.lastname: Ideker
mesh_terms: D000465:Algorithms; D016477:Artifacts; D005456:Fluorescent Dyes; D020869:Gene Expression Profiling / Q000379:methods*; D007089:Image Enhancement / Q000379:methods*; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D016013:Likelihood Functions; D036641:Microscopy, Fluorescence, Multiphoton / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
chemical_list: D005456:Fluorescent Dyes