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Bioinformatics Advance Access originally published online on December 23, 2008
Bioinformatics 2009 25(3):415-416; doi:10.1093/bioinformatics/btn647
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

arrayQualityMetrics—a bioconductor package for quality assessment of microarray data

Audrey Kauffmann 1,*, Robert Gentleman 2 and Wolfgang Huber 1

1EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and 2Computational Biology - FHCRC, 1100 Fairview Avenue North, Seattle, WA 98109, USA

*To whom correspondence should be addressed.


  Abstract

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 www.bioconductor.org. A users guide and examples are provided with the package. Some examples of HTML reports generated by arrayQualityMetrics can be found at http://www.microarray-quality.org

Contact:: audrey{at}ebi.ac.uk

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

Associate Editor: David Rocke

Received on October 1, 2008; revised on December 2, 2008; accepted on December 11, 2008

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[Abstract] [Full Text] [PDF]


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