title: A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies.
abstract: Over the last decade, gene expression microarrays have had a profound impact on biomedical research. The diversity of platforms and analytical methods available to researchers have made the comparison of data from multiple platforms challenging. In this study, we describe a framework for comparisons across platforms and laboratories. We have attempted to include nearly all the available commercial and 'in-house' platforms. Using probe sequences matched at the exon level improved consistency of measurements across the different microarray platforms compared to annotation-based matches. Generally, consistency was good for highly expressed genes, and variable for genes with lower expression values as confirmed by quantitative real-time (QRT)-PCR. Concordance of measurements was higher between laboratories on the same platform than across platforms. We demonstrate that, after stringent preprocessing, commercial arrays were more consistent than in-house arrays, and by most measures, one-dye platforms were more consistent than two-dye platforms.
authors.affiliation: Department of Developmental Biology, Harvard School of Dental Medicine, 188 Longwood Ave., Boston, Massachusetts 02115, USA. wkuo@genetics.med.harvard.edu
authors.forename: Winston Patrick
authors.initials: WP
authors.lastname: Kuo
authors.forename: Fang
authors.initials: F
authors.lastname: Liu
authors.forename: Jeff
authors.initials: J
authors.lastname: Trimarchi
authors.forename: Claudio
authors.initials: C
authors.lastname: Punzo
authors.forename: Michael
authors.initials: M
authors.lastname: Lombardi
authors.forename: Jasjit
authors.initials: J
authors.lastname: Sarang
authors.forename: Mark E
authors.initials: ME
authors.lastname: Whipple
authors.forename: Malini
authors.initials: M
authors.lastname: Maysuria
authors.forename: Kyle
authors.initials: K
authors.lastname: Serikawa
authors.forename: Sun Young
authors.initials: SY
authors.lastname: Lee
authors.forename: Donald
authors.initials: D
authors.lastname: McCrann
authors.forename: Jason
authors.initials: J
authors.lastname: Kang
authors.forename: Jeffrey R
authors.initials: JR
authors.lastname: Shearstone
authors.forename: Jocelyn
authors.initials: J
authors.lastname: Burke
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Park
authors.forename: Xiaowei
authors.initials: X
authors.lastname: Wang
authors.forename: Trent L
authors.initials: TL
authors.lastname: Rector
authors.forename: Paola
authors.initials: P
authors.lastname: Ricciardi-Castagnoli
authors.forename: Steven
authors.initials: S
authors.lastname: Perrin
authors.forename: Sangdun
authors.initials: S
authors.lastname: Choi
authors.forename: Roger
authors.initials: R
authors.lastname: Bumgarner
authors.forename: Ju Han
authors.initials: JH
authors.lastname: Kim
authors.forename: Glenn F
authors.initials: GF
authors.lastname: Short
authors.forename: Mason W
authors.initials: MW
authors.lastname: Freeman
authors.forename: Brian
authors.initials: B
authors.lastname: Seed
authors.forename: Roderick
authors.initials: R
authors.lastname: Jensen
authors.forename: George M
authors.initials: GM
authors.lastname: Church
authors.forename: Eivind
authors.initials: E
authors.lastname: Hovig
authors.forename: Connie L
authors.initials: CL
authors.lastname: Cepko
authors.forename: Peter
authors.initials: P
authors.lastname: Park
authors.forename: Lucila
authors.initials: L
authors.lastname: Ohno-Machado
authors.forename: Tor-Kristian
authors.initials: TK
authors.lastname: Jenssen
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D015342:DNA Probes / Q000737:chemistry / Q000145:classification; D020869:Gene Expression Profiling / Q000379:methods*; D046228:Microarray Analysis / Q000145:classification / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results
chemical_list: D015342:DNA Probes