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

Mark J Dunning; Mike L Smith; Matthew E Ritchie; Simon Tavaré

doi:10.1093/bioinformatics/btm311

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

Bioinformatics. 2007 Aug 15;23(16):2183-4. doi: 10.1093/bioinformatics/btm311. Epub 2007 Jun 22.

Authors

Mark J Dunning¹, Mike L Smith, Matthew E Ritchie, Simon Tavaré

Affiliation

¹ Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK. md392@cam.ac.uk

PMID: 17586828
DOI: 10.1093/bioinformatics/btm311

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Databases, Genetic
Image Interpretation, Computer-Assisted / methods*
In Situ Hybridization, Fluorescence / methods*
Microspheres
Oligonucleotide Array Sequence Analysis / methods*
Programming Languages*
Sequence Analysis, DNA / methods*
Software*