Journal Article

BASH: a tool for managing BeadArray spatial artefacts

J. M. Cairns, M. J. Dunning, M. E. Ritchie, R. Russell and A. G. Lynch

in Bioinformatics

Volume 24, issue 24, pages 2921-2922
Published in print December 2008 | ISSN: 1367-4803
Published online October 2008 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btn557

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Summary: With their many replicates and their random layouts, Illumina BeadArrays provide greater scope fordetecting spatial artefacts than do other microarray technologies. They are also robust to artefact exclusion, yet there is a lack of tools that can perform these tasks for Illumina. We present BASH, a tool for this purpose. BASH adopts the concepts of Harshlight, but implements them in a manner that utilizes the unique characteristics of the Illumina technology. Using bead-level data, spatial artefacts of various kinds can thus be identified and excluded from further analyses.

Availability: The beadarray Bioconductor package (version 1.10 onwards), www.bioconductor.org

Contact: andy.lynch@cancer.org.uk

Supplementary information: Additional information and a vignette are included in the beadarray package.

Journal Article.  1646 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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