Gene expression Quick and simple: quality control of microarray data

Motivation: Microarrays are high-throughput tools for parallel mini-aturized 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 com-pares 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 meas-ures of spot quality also reflect the quality of protocols, they were employed to find the optimal print buffer in an optimization experi-ment. 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