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Bioinformatics Advance Access published online on June 22, 2007
Bioinformatics, 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 a,*, Mike L. Smith a, Matthew E. Ritchie a and Simon Tavaré a

aDepartment of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, United Kingdom

*to whom correspondence should be addressed. Mr. Mark Dunning, E-mail: md392{at}cam.ac.uk


  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 normalisation 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 summarised and stored in a format which can be used by other R/Bioconductor packages to perform downstream analyses. Summarised 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.

Associate Editor: Prof. Alfonso Valencia

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

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