Skip Navigation


Bioinformatics Advance Access originally published online on September 13, 2005
Bioinformatics 2005 21(21):3983-3989; doi:10.1093/bioinformatics/bti665
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
21/21/3983    most recent
bti665v1
Right arrow Alert me when this article is cited
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 (12)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Zhou, L.
Right arrow Articles by Rocke, D. M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Zhou, L.
Right arrow Articles by Rocke, D. M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

An expression index for Affymetrix GeneChips based on the generalized logarithm

Lei Zhou 1 and David M. Rocke 2,*

1Department of Biostatistics, Amgen, Inc. USA
2Division of Biostatistics, University of California Davis, CA, USA

*To whom correspondence should be addressed.

Motivation: Affymetrix GeneChip high-density oligonucleotide arrays interrogate a single transcript using multiple short 25mer probes. Usually, a necessary step in the analysis of experiments using these GeneChips is to summarize each of these probe sets into a single expression index that can then be used for determining differential expression, for classification, for clustering, and for other analyses. In this paper, we propose a new expression index that is competitive with the best existing methods, and superior in many cases. We call this expression index method GLA, for GLog Average, since after normalization at the probe level, we take the mean generalized logarithm of perfect match probes.

Results: In this paper, we use Affycomp as the primary tool to assess the weaknesses and strengths of GLA. Comparisons are made between GLA and most widely used summary methods (RMA, MAS5.0 and MBEI) in great detail. The substantial reduction in variability and increased ability to detect differential expression, together with the simplicity of implementation, make GLA a plausible candidate for analysis of Affymetrix GeneChip data.

Contact: dmrocke{at}ucdavis.edu

Received on June 4, 2005; revised on August 26, 2005; accepted on September 5, 2005

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
 BioinformaticsHome page
H. Bengtsson, R. Irizarry, B. Carvalho, and T. P. Speed
Estimation and assessment of raw copy numbers at the single locus level
Bioinformatics, March 15, 2008; 24(6): 759 - 767.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
D. Zhu, Y. Li, and H. Li
Multivariate correlation estimator for inferring functional relationships from replicated genome-wide data
Bioinformatics, September 1, 2007; 23(17): 2298 - 2305.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
D. S. Yuan and R. A. Irizarry
High-resolution spatial normalization for microarrays containing embedded technical replicates
Bioinformatics, December 15, 2006; 22(24): 3054 - 3060.
[Abstract] [Full Text] [PDF]

Home page
 Physiol. GenomicsHome page
T. S. Mehta, S. O. Zakharkin, G. L. Gadbury, and D. B. Allison
Epistemological issues in omics and high-dimensional biology: give the people what they want
Physiol Genomics, December 13, 2006; 28(1): 24 - 32.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
Z. Goldberg, D. M. Rocke, C. Schwietert, S. R. Berglund, A. Santana, A. Jones, J. Lehmann, R. Stern, R. Lu, and C. Hartmann Siantar
Human In vivo Dose-Response to Controlled, Low-Dose Low Linear Energy Transfer Ionizing Radiation Exposure.
Clin. Cancer Res., June 15, 2006; 12(12): 3723 - 3729.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
R. A. Irizarry, Z. Wu, and H. A. Jaffee
Comparison of Affymetrix GeneChip expression measures
Bioinformatics, April 1, 2006; 22(7): 789 - 794.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
D. M. Rocke, Z. Goldberg, C. Schweitert, and A. Santana
A method for detection of differential gene expression in the presence of inter-individual variability in response
Bioinformatics, November 1, 2005; 21(21): 3990 - 3992.
[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.