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.
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.
Authors: Keith Noto; Saeed Majidi; Andrea G Edlow; Heather C Wick; Diana W Bianchi; Donna K Slonim Journal: J Comput Biol Date: 2015-02-04 Impact factor: 1.479
Authors: Max Bylesjö; Daniel Eriksson; Andreas Sjödin; Michael Sjöström; Stefan Jansson; Henrik Antti; Johan Trygg Journal: BMC Bioinformatics Date: 2005-10-13 Impact factor: 3.169
Authors: Song Yang; Xiang Guo; Yaw-Ching Yang; Denise Papcunik; Caroline Heckman; Jeffrey Hooke; Craig D Shriver; Michael N Liebman; Hai Hu Journal: Cancer Inform Date: 2007-02-24