Journal Article

arrayQualityMetrics—a bioconductor package for quality assessment of microarray data

Audrey Kauffmann, Robert Gentleman and Wolfgang Huber

in Bioinformatics

Volume 25, issue 3, pages 415-416
Published in print February 2009 | ISSN: 1367-4803
Published online December 2008 | e-ISSN: 1460-2059 | DOI:

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Summary:: The assessment of data quality is a major concern in microarray analysis. arrayQualityMetrics is a Bioconductor package that provides a report with diagnostic plots for one or two colour microarray data. The quality metrics assess reproducibility, identify apparent outlier arrays and compute measures of signal-to-noise ratio. The tool handles most current microarray technologies and is amenable to use in automated analysis pipelines or for automatic report generation, as well as for use by individuals. The diagnosis of quality remains, in principle, a context-dependent judgement, but our tool provides powerful, automated, objective and comprehensive instruments on which to base a decision.

Availability:: arrayQualityMetrics is a free and open source package, under LGPL license, available from the Bioconductor project at A users guide and examples are provided with the package. Some examples of HTML reports generated by arrayQualityMetrics can be found at


Supplementary information:: Supplementary data are available at Bioinformatics online.

Journal Article.  1121 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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