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

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


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

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Computational Biology / methods*
  • Data Interpretation, Statistical
  • Internet
  • Oligonucleotide Array Sequence Analysis / methods
  • Oligonucleotide Array Sequence Analysis / standards*
  • Quality Control
  • Software*