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Bioinformatics. 2008 Dec 15;24(24):2921-2. doi: 10.1093/bioinformatics/btn557. Epub 2008 Oct 25.

BASH: a tool for managing BeadArray spatial artefacts.

Author information

  • 1Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB20RE, UK.

Abstract

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

PMID:
18953044
[PubMed - indexed for MEDLINE]
PMCID:
PMC2639304
Free PMC Article
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