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Bioinformatics Advance Access first published online on December 21, 2004
This version published online on February 2, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti238
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Bioinformatics © Oxford University Press 2004; all rights reserved.
Received June 2, 2004
Revised November 29, 2004
Accepted December 15, 2004

Article

Quick & simple: quality control of microarray data

Ursula Sauer 1*, Claudia Preininger 1, and Robert Hany-Schmatzberger 1

1 ARC Seibersdorf Research GmbH, Division Bio-resources, Biotechnology Unit, A-2444 Seibersdorf, Austria

* To whom correspondence should be addressed.
Ursula Sauer, E-mail: Ursula.Sauer{at}arcs.ac.at


  Abstract

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 of 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 are also reflecting 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 are suitable to replace the visual inspection of slides.


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