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Bioinformatics Advance Access originally published online on February 2, 2006
Bioinformatics 2006 22(7):897-899; 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
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affylmGUI: a graphical user interface for linear modeling of single channel microarray data

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

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

*To whom correspondence should be addressed.

Summary: affylmGUI is a graphical user interface (GUI) to an integrated workflow for Affymetrix microarray data. The user is able to proceed from raw data (CEL files) to QC and pre-processing, 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 Mac OS/X with X11. Further documentation is available at http://bioinf.wehi.edu.au/affylmGUI

Contact: keith{at}wehi.edu.au

Received on November 17, 2005; revised on January 23, 2006; accepted on January 23, 2006

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