title: Standardizing global gene expression analysis between laboratories and across platforms.
abstract: To facilitate collaborative research efforts between multi-investigator teams using DNA microarrays, we identified sources of error and data variability between laboratories and across microarray platforms, and methods to accommodate this variability. RNA expression data were generated in seven laboratories, which compared two standard RNA samples using 12 microarray platforms. At least two standard microarray types (one spotted, one commercial) were used by all laboratories. Reproducibility for most platforms within any laboratory was typically good, but reproducibility between platforms and across laboratories was generally poor. Reproducibility between laboratories increased markedly when standardized protocols were implemented for RNA labeling, hybridization, microarray processing, data acquisition and data normalization. Reproducibility was highest when analysis was based on biological themes defined by enriched Gene Ontology (GO) categories. These findings indicate that microarray results can be comparable across multiple laboratories, especially when a common platform and set of procedures are used.
authors.forename: Theodore
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authors.lastname: Bammler
authors.forename: Richard P
authors.initials: RP
authors.lastname: Beyer
authors.forename: Sanchita
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authors.lastname: Bhattacharya
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authors.lastname: Boorman
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authors.forename: Blair U
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authors.lastname: Deng
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authors.lastname: Palmer
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authors.forename: Charles M
authors.initials: CM
authors.lastname: Perou
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authors.lastname: Phillips
authors.forename: Li-Xuan
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authors.lastname: Qin
authors.forename: Yang
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authors.lastname: Qiu
authors.forename: Sean D
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authors.lastname: Quigley
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authors.lastname: Rusyn
authors.forename: Leona D
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authors.lastname: Samson
authors.forename: David A
authors.initials: DA
authors.lastname: Schwartz
authors.forename: Yan
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authors.lastname: Shi
authors.forename: Jung-Lim
authors.initials: JL
authors.lastname: Shin
authors.forename: Stella O
authors.initials: SO
authors.lastname: Sieber
authors.forename: Susan
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authors.lastname: Slifer
authors.forename: Marcy C
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authors.lastname: Speer
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authors.forename: Dean I
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authors.lastname: Sproles
authors.forename: James A
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authors.forename: William A
authors.initials: WA
authors.lastname: Suk
authors.forename: Robert C
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authors.forename: Signe A
authors.initials: SA
authors.lastname: Todd
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authors.initials: CJ
authors.lastname: Tucker
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authors.lastname: Van Houten
authors.forename: Brenda K
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authors.lastname: Weis
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authors.lastname: Xuan
authors.forename: Helmut
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authors.lastname: Zarbl
mesh_terms: D020869:Gene Expression Profiling / Q000592:standards*; D007753:Laboratories / Q000592:standards; D020411:Oligonucleotide Array Sequence Analysis / Q000592:standards*; D015203:Reproducibility of Results