title: Multiple-laboratory comparison of microarray platforms.
abstract: Microarray technology is a powerful tool for measuring RNA expression for thousands of genes at once. Various studies have been published comparing competing platforms with mixed results: some find agreement, others do not. As the number of researchers starting to use microarrays and the number of cross-platform meta-analysis studies rapidly increases, appropriate platform assessments become more important. Here we present results from a comparison study that offers important improvements over those previously described in the literature. In particular, we noticed that none of the previously published papers consider differences between labs. For this study, a consortium of ten laboratories from the Washington, DC-Baltimore, USA, area was formed to compare data obtained from three widely used platforms using identical RNA samples. We used appropriate statistical analysis to demonstrate that there are relatively large differences in data obtained in labs using the same platform, but that the results from the best-performing labs agree rather well.
authors.affiliation: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA. rafa@jhu.edu
authors.forename: Rafael A
authors.initials: RA
authors.lastname: Irizarry
authors.forename: Daniel
authors.initials: D
authors.lastname: Warren
authors.forename: Forrest
authors.initials: F
authors.lastname: Spencer
authors.forename: Irene F
authors.initials: IF
authors.lastname: Kim
authors.forename: Shyam
authors.initials: S
authors.lastname: Biswal
authors.forename: Bryan C
authors.initials: BC
authors.lastname: Frank
authors.forename: Edward
authors.initials: E
authors.lastname: Gabrielson
authors.forename: Joe G N
authors.initials: JG
authors.lastname: Garcia
authors.forename: Joel
authors.initials: J
authors.lastname: Geoghegan
authors.forename: Gregory
authors.initials: G
authors.lastname: Germino
authors.forename: Constance
authors.initials: C
authors.lastname: Griffin
authors.forename: Sara C
authors.initials: SC
authors.lastname: Hilmer
authors.forename: Eric
authors.initials: E
authors.lastname: Hoffman
authors.forename: Anne E
authors.initials: AE
authors.lastname: Jedlicka
authors.forename: Ernest
authors.initials: E
authors.lastname: Kawasaki
authors.forename: Francisco
authors.initials: F
authors.lastname: Martínez-Murillo
authors.forename: Laura
authors.initials: L
authors.lastname: Morsberger
authors.forename: Hannah
authors.initials: H
authors.lastname: Lee
authors.forename: David
authors.initials: D
authors.lastname: Petersen
authors.forename: John
authors.initials: J
authors.lastname: Quackenbush
authors.forename: Alan
authors.initials: A
authors.lastname: Scott
authors.forename: Michael
authors.initials: M
authors.lastname: Wilson
authors.forename: Yanqin
authors.initials: Y
authors.lastname: Yang
authors.forename: Shui Qing
authors.initials: SQ
authors.lastname: Ye
authors.forename: Wayne
authors.initials: W
authors.lastname: Yu
mesh_terms: D015142:Baltimore; D004219:District of Columbia; D020869:Gene Expression Profiling / Q000592:standards; D006801:Humans; D007753:Laboratories / Q000592:standards; D020411:Oligonucleotide Array Sequence Analysis / Q000592:standards*; D015203:Reproducibility of Results