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Bioinformatics Advance Access originally published online on June 22, 2007
Bioinformatics 2007 23(16):2183-2184; doi:10.1093/bioinformatics/btm311
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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

Mark J. Dunning *, Mike L. Smith , Matthew E. Ritchie and Simon Tavaré

Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK

*To whom correspondence should be addressed.


  Abstract

Summary: 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.

Contact: md392{at}cam.ac.uk

Associate Editor: Alfonso Valencia

Received on April 12, 2007; revised on May 22, 2007; accepted on June 4, 2007

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