title: Best practices for hybridization design in two-colour microarray analysis.
abstract: Two-colour microarrays are a popular platform of choice in gene expression studies. Because two different samples are hybridized on a single microarray, and several microarrays are usually needed in a given experiment, there are many possible ways to combine samples on different microarrays. The actual combination employed is commonly referred to as the 'hybridization design'. Different types of hybridization designs have been developed, all aimed at optimizing the experimental setup for the detection of differentially expressed genes while coping with technical noise. Here, we first provide an overview of the different classes of hybridization designs, discussing their advantages and limitations, and then we illustrate the current trends in the use of different hybridization design types in contemporary research.
authors.affiliation: Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium. dries.knapen@ua.ac.be
authors.forename: Dries
authors.initials: D
authors.lastname: Knapen
authors.forename: Lucia
authors.initials: L
authors.lastname: Vergauwen
authors.forename: Kris
authors.initials: K
authors.lastname: Laukens
authors.forename: Ronny
authors.initials: R
authors.lastname: Blust
mesh_terms: D003116:Color; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D013194:Staining and Labeling / Q000379:methods