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Bioinformatics Advance Access published online on February 2, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl025
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received November 17, 2005
Revised January 23, 2006
Accepted January 23, 2006

Applications note

affylmGUI: a graphical user interface for linear modeling of single channel microarray data

James M. Wettenhall 1, Ken M. Simpson 1, Keith Satterley 1 *, and Gordon K. Smyth 1

1 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, Parkville, 3050, Australia

* To whom correspondence should be addressed.
Keith Satterley, E-mail: keith{at}wehi.edu.au


  Abstract

Summary: affylmGUI is a graphical user interface to an integrated workflow for Affymetrix microarray data. The user is able to proceed from raw data (CEL files) to QC and preprocessing, and eventually to analysis of differential expression using linear models with empirical Bayes smoothing. Output of the analysis (tables and figures) can be exported to an HTML report. The GUI provides user-friendly access to state-of-the-art methods embodied in the Bioconductor software repository.

Availability: affylmGUI is an R package freely available from http://www.bioconductor.org. It requires R version 1.9.0 or later and tcl/tk 8.3 or later and has been successfully tested on Windows 2000, Windows XP, Linux (RedHat and Fedora distributions), and on Mac OS/X with X11. Further documentation is available at http://bioinf.wehi.edu.au/affylmGUI.

Associate Editor: David Rocke
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