A package that provides a report with diagnostic plots for one or two colour microarray data. After preparation of the data, a single command line is used to create the report. The quality metrics assess reproducibility, identify apparent outlier arrays and compute measures of signal-to-noise ratio. arrayQualityMetrics 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. Its main benefits are its simplicity of use, the ability to have the same report for different types of platforms, and the opportunity for users or developers to extend it for their needs. arrayQualityMetrics can be used for individual data analyses or in routine data production pipelines, to provide fast uniform reporting. The diagnosis of quality remains, in principle, a context-dependent judgement, but this tool provides powerful, automated, objective and comprehensive instruments on which to base a decision.