title: Adaptable gene-specific dye bias correction for two-channel DNA microarrays.
abstract: DNA microarray technology is a powerful tool for monitoring gene expression or for finding the location of DNA-bound proteins. DNA microarrays can suffer from gene-specific dye bias (GSDB), causing some probes to be affected more by the dye than by the sample. This results in large measurement errors, which vary considerably for different probes and also across different hybridizations. GSDB is not corrected by conventional normalization and has been difficult to address systematically because of its variance. We show that GSDB is influenced by label incorporation efficiency, explaining the variation of GSDB across different hybridizations. A correction method (Gene- And Slide-Specific Correction, GASSCO) is presented, whereby sequence-specific corrections are modulated by the overall bias of individual hybridizations. GASSCO outperforms earlier methods and works well on a variety of publically available datasets covering a range of platforms, organisms and applications, including ChIP on chip. A sequence-based model is also presented, which predicts which probes will suffer most from GSDB, useful for microarray probe design and correction of individual hybridizations. Software implementing the method is publicly available.
authors.affiliation: Department of Physiological Chemistry, University Medical Center Utrecht, Universiteitsweg, Utrecht, The Netherlands.
authors.forename: Thanasis
authors.initials: T
authors.lastname: Margaritis
authors.forename: Philip
authors.initials: P
authors.lastname: Lijnzaad
authors.forename: Dik
authors.initials: D
authors.lastname: van Leenen
authors.forename: Diane
authors.initials: D
authors.lastname: Bouwmeester
authors.forename: Patrick
authors.initials: P
authors.lastname: Kemmeren
authors.forename: Sander R
authors.initials: SR
authors.lastname: van Hooff
authors.forename: Frank C P
authors.initials: FC
authors.lastname: Holstege
mesh_terms: D016477:Artifacts; D001483:Base Sequence; D015982:Bias; D004396:Coloring Agents / Q000032:analysis / Q000378:metabolism*; D005796:Genes; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards*; D013194:Staining and Labeling / Q000592:standards*
chemical_list: D004396:Coloring Agents