Quick and simple: quality control of microarray data.
BACKGROUND
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.


BACKGROUND
Ursula.Sauer@arcs.ac.at.
Sauer
Ursula
U
ARC Seibersdorf research GmbH, Department Bio-resources, A-2444 Seibersdorf, Austria. Ursula.Sauer@arcs.ac.at
Preininger
Claudia
C
Hany-Schmatzberger
Robert
R
D000465:Algorithms; D019985:Benchmarking / Q000379:methods; D020869:Gene Expression Profiling / Q000379:methods*; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards; D011786:Quality Control; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity