Bioinformatics. 2007 Aug 15;23(16):2183-4. Epub 2007 Jun 22.

beadarray: R classes and methods for Illumina bead-based data.

Dunning MJ, Smith ML, Ritchie ME, Tavaré S.

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Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK. md392@cam.ac.uk

Abstract

The R/Bioconductor package beadarray allows raw data from Illumina experiments to be read and stored in convenient R classes. Users are free to choose between various methods of image processing, background correction and normalization in their analysis rather than using the defaults in Illumina's; proprietary software. The package also allows quality assessment to be carried out on the raw data. The data can then be summarized and stored in a format which can be used by other R/Bioconductor packages to perform downstream analyses. Summarized data processed by Illumina's; BeadStudio software can also be read and analysed in the same manner. Availability: The beadarray package is available from the Bioconductor web page at www.bioconductor.org. A user's guide and example data sets are provided with the package.

PMID:: 17586828; [PubMed - indexed for MEDLINE]

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