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Bioinformatics Advance Access originally published online on June 8, 2009
Bioinformatics 2009 25(16):2092-2094; doi:10.1093/bioinformatics/btp354
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© 2009 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.

Importing ArrayExpress datasets into R/Bioconductor

Audrey Kauffmann 1,*, Tim F. Rayner 2, Helen Parkinson 1, Misha Kapushesky 1, Margus Lukk 1, Alvis Brazma 1 and Wolfgang Huber 1

1EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD and 2Cambridge Institute for Medical Research, Addenbrooke's Hospital, Cambridge CB2 0XY, UK

*To whom correspondence should be addressed.


  Abstract

Summary:ArrayExpress is one of the largest public repositories of microarray datasets. R/Bioconductor provides a comprehensive suite of microarray analysis and integrative bioinformatics software. However, easy ways for importing datasets from ArrayExpress into R/Bioconductor have been lacking. Here, we present such a tool that is suitable for both interactive and automated use.

Availability: The ArrayExpress package is available from the Bioconductor project at http://www.bioconductor.org. A users guide and examples are provided with the package.

Contact: audrey{at}ebi.ac.uk

Supplementary information:Supplementary data are available Bioinformatics online.

Associate Editor: Jonathan Wren

Received on April 21, 2009; revised on May 28, 2009; accepted on May 31, 2009

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