Skip Navigation

This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
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 (25)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Durbin, B.
Right arrow Articles by Rocke, D. M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Durbin, B.
Right arrow Articles by Rocke, D. M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics Vol. 19 no. 11 2003
Pages 1360-1367
© 2003 Oxford University Press

Estimation of transformation parameters for microarray data

Blythe Durbin 1,* and David M. Rocke 2

1 Department of Statistics
2 Department of Applied Science, UC Davis, Davis, CA 95616, USA

Received on September 9, 2002 ; revised on February 19, 2003 ; accepted on February 21, 2003

Motivation and Results: Durbin et al. (2002), Huber et al. (2002) and Munson (2001) independently introduced a family of transformations (the generalized-log family) which stabilizes the variance of microarray data up to the first order. We introduce a method for estimating the transformation parameter in tandem with a linear model based on the procedure outlined in Box and Cox (1964). We also discuss means of finding transformations within the generalized-log family which are optimal under other criteria, such as minimum residual skewness and minimum mean-variance dependency.

Availability: R and Matlab code and test data are available from the authors on request.

Contact: bpdurbin{at}ucdavis.edu

* To whom correspondence should be addressed.


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
 Nucleic Acids ResHome page
S. M. Lin, P. Du, W. Huber, and W. A. Kibbe
Model-based variance-stabilizing transformation for Illumina microarray data
Nucleic Acids Res., February 2, 2008; 36(2): e11 - e11.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
E. S. Motakis, G. P. Nason, P. Fryzlewicz, and G. A. Rutter
Variance stabilization and normalization for one-color microarray data using a data-driven multiscale approach
Bioinformatics, October 15, 2006; 22(20): 2547 - 2553.
[Abstract] [Full Text] [PDF]

Home page
 BrainHome page
S. Jamali, F. Bartolomei, A. Robaglia-Schlupp, A. Massacrier, J.-C. Peragut, J. Regis, H. Dufour, R. Ravid, P. Roll, S. Pereira, et al.
Large-scale expression study of human mesial temporal lobe epilepsy: evidence for dysregulation of the neurotransmission and complement systems in the entorhinal cortex
Brain, March 1, 2006; 129(3): 625 - 641.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
M. R. Khondoker, C. A. Glasbey, and B. J. Worton
Statistical estimation of gene expression using multiple laser scans of microarrays
Bioinformatics, January 15, 2006; 22(2): 215 - 219.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
G. J. G. Upton and J. C. Lloyd
Oligonucleotide arrays: information from replication and spatial structure
Bioinformatics, November 15, 2005; 21(22): 4162 - 4168.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
L. Zhou and D. M. Rocke
An expression index for Affymetrix GeneChips based on the generalized logarithm
Bioinformatics, November 1, 2005; 21(21): 3983 - 3989.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
E. Tamoto, M. Tada, K. Murakawa, M. Takada, G. Shindo, K.-i. Teramoto, A. Matsunaga, K. Komuro, M. Kanai, A. Kawakami, et al.
Gene-Expression Profile Changes Correlated with Tumor Progression and Lymph Node Metastasis in Esophageal Cancer
Clin. Cancer Res., June 1, 2004; 10(11): 3629 - 3638.
[Abstract] [Full Text] [PDF]

Home page
 Physiol. GenomicsHome page
J. Z. Pan, R. Jornsten, and R. P. Hart
Screening anti-inflammatory compounds in injured spinal cord with microarrays: a comparison of bioinformatics analysis approaches
Physiol Genomics, April 13, 2004; 17(2): 201 - 214.
[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.