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Bioinformatics Advance Access originally published online on July 10, 2007
Bioinformatics 2007 23(18):2493-2494; doi:10.1093/bioinformatics/btm357
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

RefPlus: an R package extending the RMA Algorithm

Chris Harbron 1,*, Kai-Ming Chang 2 and Marie C. South 3

1Statistical Sciences, AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK, 2Department of Research, Koo Foundation Sun Yat-Sen Cancer Center, 125 Lihder Road, Taipei 112, Taiwan and 3Cancer Discovery Medicine, AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK

*To whom correspondence should be addressed.


  Abstract

Summary: RMA has become a widely used methodology to pre-process Affymetrix gene expression microarrays. A limitation of RMA is that the calculated probeset intensities change when a set of microarrays is re-pre-processed after the inclusion of additional microarrays into the analysis set. Here we report the availability of the RefPlus package containing functions to perform the Extrapolation Strategy and Extrapolation Averaging algorithms which address these issues.

Availability: The software is implemented in the R language and can be downloaded from the Bioconductor project website (http://www.bioconductor.org).

Contact: Chris.Harbron{at}AstraZeneca.Com

Supplementary information: Further details of the workings and evaluation of these functions are given in the documentation available on the Bioconductor website.

Associate Editor: David Rocke

Received on May 25, 2007; revised on June 25, 2007; accepted on July 4, 2007

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