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Bioinformatics Advance Access originally published online on August 25, 2009
Bioinformatics 2009 25(22):3033-3034; doi:10.1093/bioinformatics/btp514
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

digeR: a graphical user interface R package for analyzing 2D-DIGE data

Yue Fan 1,2, T. Brendan Murphy 3 and R. William G. Watson 1,2,*

1UCD School of Medicine and Medical Science, 2UCD Conway Institute of Biomolecular and Biomolecular Research and 3UCD School of Mathematical Sciences, University College Dublin, Dublin 4, Dublin, Ireland

*To whom correspondence should be addressed.


  Abstract

Summary: 2D Difference In-Gel Electrophoresis (2D-DIGE) or 2D gel technology is being used as a routine proteomics technique for biomarker discovery. Analyzing such high-dimensional data requires multivariate analysis techniques to be applied. In addition, protein post-translational modification (PTM) information from the 2D gel data is usually overlooked. We report on an R package, digeR, with an easy to use graphical user interface for analyzing 2D-DIGE (2D gel) data. It provides a tool for visually looking for potential PTM changes from different biological states and support biomarker discovery through multivariate analysis techniques.

Availability: digeR package is freely available from the CRAN: http://cran.r-project.org/web/packages/digeR/index.html.

Contact: yue.fan{at}ucd.ie

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: John Quackenbush

Received on June 24, 2009; revised on August 20, 2009; accepted on August 21, 2009

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