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Article
Nature Methods - 2, 351 - 356 (2005)
Published online: 21 April 2005; | doi:10.1038/nmeth754


There is an Addendum (June 2005) associated with this Article.

There is an Addendum (June 2005) associated with this Article.

There is an Addendum (June 2005) associated with this Article.

There is an Addendum (June 2005) associated with this Article.

There is an Addendum (June 2005) associated with this Article.

There is an Addendum (June 2005) associated with this Article.

There is an Addendum (June 2005) associated with this Article.

There is an Addendum (June 2005) associated with this Article.

There is an Addendum (June 2005) associated with this Article.

Standardizing global gene expression analysis between laboratories and across platforms

Members of the Toxicogenomics Research Consortium

A list of authors and their affiliations appears in the Supplementary Note online.

Correspondence should be addressed to B.K. Weis weis@niehs.nih.gov

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.

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Nature Methods
ISSN: 1548-7091
EISSN: 1548-7105
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