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Quick and simple: quality control of microarray data.

Sauer U, Preininger C, Hany-Schmatzberger R

ARC Seibersdorf research GmbH, Department Bio-resources, A-2444 Seibersdorf, Austria. Ursula.Sauer@arcs.ac.at

MOTIVATION: Microarrays are high-throughput tools for parallel miniaturized detection of biomolecules. In contrast to experiments using ratios of signals in two channels, experiments with only one fluorescent dye cause special problems for data analysis. The present work compares algorithms for quality filtering on spot level as well as array/slide level. RESULTS: Methods for quantitative spot filtering are discussed and new sets of quality scores for data preprocessing are designed. As measures of spot quality also reflect the quality of protocols, they were employed to find the optimal print buffer in an optimization experiment. In order to determine problematic arrays within a set of replicates we tested methods of outlier detection which can suitably replace the visual inspection of slides. CONTACT: Ursula.Sauer@arcs.ac.at.

Published 11 April 2005 in Bioinformatics, 21(8): 1572-8.
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