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

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

Fig. 1.

(a) MA-plot for an Agilent microarray. The M-values are not centered on zero meaning that there is a dependency between the intensities and the log-ratio. (b) Spatial distribution of the background of the green channel for an Illumina chip. There is an abnormal distribution of high intensities at the top border of the array. (c) Density plot of the log-intensities of an Affymetrix set of arrays (E-GEOD-349 ArrayExpress set). The density of one of the arrays is shifted on the x-axis. (d) Heatmap of the ArrayExpress Affymetrix data set E-GEOD-1571. Array 18 is an outlier.