Quick and simple: Quality control of microarray data

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 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 orderto determine problematic arrays within a set of replicates we tested methods of outlier detection which can suitably replace the visual inspection of slides. © The Author 2004. Published by Oxford University Press. All rights reserved.