A Framework for Determining Outlying Microarray Experiments

Raymond Wan[1] (rwan@kuicr.kyoto-u.ac.jp)
├ůsa M. Wheelock[2] (asa@para-docs.org)
Hiroshi Mamitsuka[1] (mami@kuicr.kyoto-u.ac.jp)

[1] Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, 611-0011, Japan
[2] Lung Research Lab L4:01, Respiratory Medicine Unit, Department of Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden


Microarrays are high-throughput technologies whose data are known to be noisy. In this work, we propose a graph-based method which first identifies the extent to which a single microarray experiment is noisy and then applies an error function to clean individual expression levels. These two steps are unified within a framework based on a graph representation of a separate data set from some repository. We demonstrate the utility of our method by comparing our results against statistical methods by applying both techniques to simulated microarray data. Our results are encouraging and indicate one potential use of microarray data from past experiments.

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Japanese Society for Bioinformatics