Microarray quality metrics
Although microarrays are widely used and the interest in expression data is increasing with the appearance of new applications, the assessment of data quality remains a major concern. Microarray data quality can be affected by several factors at each step of the microarray experiment processing. The effects of some variability sources such as dye or gene effects can be corrected by normalisation procedures, whereas others remain there as noise. The assessment of data quality is an integral part of the microarray analysis process.
A tool for quality assessment
The objective of this project is to develop and disseminate quality metrics and tools for determining data quality. We have developed a Bioconductor package, named arrayQualityMetrics, that provides a HTML report with diagnostic plots for one or dual colour microarray data. The quality report assesses batch effects as well as individual array quality, spatial effects and a number of other metrics. The report is intended to be used as a first step of a microarray analysis.
Examples
Here are links to some examples of HTML reports produced by arrayQualityMetrics:
Related Links
If you have any query concerning the package, please contact Wolfgang Huber.