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Bioinformatics. 2009 Feb 1;25(3):415-6. doi: 10.1093/bioinformatics/btn647. Epub 2008 Dec 23.

arrayQualityMetrics--a bioconductor package for quality assessment of microarray data.

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1
EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. audrey@ebi.ac.uk

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

PMID:
19106121
PMCID:
PMC2639074
DOI:
10.1093/bioinformatics/btn647
[Indexed for MEDLINE]
Free PMC Article
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