Skip Navigation


Bioinformatics Advance Access originally published online on February 2, 2006
Bioinformatics 2006 22(7):897-899; doi:10.1093/bioinformatics/btl025
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrowOA All Versions of this Article:
22/7/897    most recent
btl025v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (15)
Google Scholar
Right arrow Articles by Wettenhall, J. M.
Right arrow Articles by Smyth, G. K.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Wettenhall, J. M.
Right arrow Articles by Smyth, G. K.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

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

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Plant Cell PhysiolHome page
N. Nishimura, M. Okamoto, M. Narusaka, M. Yasuda, H. Nakashita, K. Shinozaki, Y. Narusaka, and T. Hirayama
ABA Hypersensitive Germination2-1 Causes the Activation of Both Abscisic Acid and Salicylic Acid Responses in Arabidopsis
Plant Cell Physiol., December 1, 2009; 50(12): 2112 - 2122.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
J. Garbarino, M. Padamsee, L. Wilcox, P. M. Oelkers, D. D'Ambrosio, K. V. Ruggles, N. Ramsey, O. Jabado, A. Turkish, and S. L. Sturley
Sterol and Diacylglycerol Acyltransferase Deficiency Triggers Fatty Acid-mediated Cell Death
J. Biol. Chem., November 6, 2009; 284(45): 30994 - 31005.
[Abstract] [Full Text] [PDF]

Home page
 Mol PlantHome page
I. Pandelova, M. F. Betts, V. A. Manning, L. J. Wilhelm, T. C. Mockler, and L. M. Ciuffetti
Analysis of Transcriptome Changes Induced by Ptr ToxA in Wheat Provides Insights into the Mechanisms of Plant Susceptibility
Mol Plant, September 1, 2009; 2(5): 1067 - 1083.
[Abstract] [Full Text] [PDF]

Home page
 J EndocrinolHome page
L Lundholm, G Bryzgalova, H Gao, N Portwood, S Falt, K D Berndt, A Dicker, D Galuska, J R Zierath, J-A Gustafsson, et al.
The estrogen receptor {alpha}-selective agonist propyl pyrazole triol improves glucose tolerance in ob/ob mice; potential molecular mechanisms
J. Endocrinol., November 1, 2008; 199(2): 275 - 286.
[Abstract] [Full Text] [PDF]

Home page
 Biol. Reprod.Home page
V. Thimon, E. Calvo, O. Koukoui, C. Legare, and R. Sullivan
Effects of Vasectomy on Gene Expression Profiling along the Human Epididymis
Biol Reprod, August 1, 2008; 79(2): 262 - 273.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
M. C. Lopez-Martin, M. Becana, L. C. Romero, and C. Gotor
Knocking Out Cytosolic Cysteine Synthesis Compromises the Antioxidant Capacity of the Cytosol to Maintain Discrete Concentrations of Hydrogen Peroxide in Arabidopsis
Plant Physiology, June 1, 2008; 147(2): 562 - 572.
[Abstract] [Full Text] [PDF]

Home page
 J AndrolHome page
J. S. Barthold, S. M. Mccahan, A. V. Singh, T. B. Knudsen, X. Si, L. Campion, and R. E. Akins
Altered Expression of Muscle- and Cytoskeleton-Related Genes in a Rat Strain With Inherited Cryptorchidism
J Androl, May 1, 2008; 29(3): 352 - 366.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
V. Bourdeau, J. Deschenes, D. Laperriere, M. Aid, J. H. White, and S. Mader
Mechanisms of primary and secondary estrogen target gene regulation in breast cancer cells
Nucleic Acids Res., January 17, 2008; 36(1): 76 - 93.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
R. Sanges, F. Cordero, and R. A. Calogero
oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language
Bioinformatics, December 15, 2007; 23(24): 3406 - 3408.
[Abstract] [Full Text] [PDF]

Home page
 Mol Hum ReprodHome page
V. Thimon, O. Koukoui, E. Calvo, and R. Sullivan
Region-specific gene expression profiling along the human epididymis
Mol. Hum. Reprod., October 1, 2007; 13(10): 691 - 704.
[Abstract] [Full Text] [PDF]

Home page
 Plant Cell PhysiolHome page
Y. Manabe, N. Tinker, A. Colville, and B. Miki
CSR1, the Sole Target of Imidazolinone Herbicide in Arabidopsis thaliana
Plant Cell Physiol., September 1, 2007; 48(9): 1340 - 1358.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
C. Tian, E. Chikayama, Y. Tsuboi, T. Kuromori, K. Shinozaki, J. Kikuchi, and T. Hirayama
Top-down Phenomics of Arabidopsis thaliana: METABOLIC PROFILING BY ONE- AND TWO-DIMENSIONAL NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND TRANSCRIPTOME ANALYSIS OF ALBINO MUTANTS
J. Biol. Chem., June 22, 2007; 282(25): 18532 - 18541.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.