Bioinformatics Vol. 19 no. 8 2003
Pages 966-972
© 2003 Oxford University Press
Approximate variance-stabilizing transformations for gene-expression microarray data
1 Department of Applied Science, University
of California, Davis, Davis, CA 95616
2 Department of Statistics, University of
California, Davis, Davis, CA 95616, USA
Received on August 20, 2002
; revised on October 20, 2002
; accepted on November 1, 2002
Motivation: A variance stabilizing transformation for microarray data was recently introduced independently by several research groups. This transformation has sometimes been called the generalized logarithm or glog transformation. In this paper, we derive several alternative approximate variance stabilizing transformations that may be easier to use in some applications.
Results: We demonstrate that the started-log and the log-linear-hybrid transformation families can produce approximate variance stabilizing transformations for microarray data that are nearly as good as the generalized logarithm (glog) transformation. These transformations may be more convenient in some applications.
Contact: dmrocke{at}ucdavis.edu
* To whom correspondence should be addressed.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  A. W. Dowsey, M. J. Dunn, and G.-Z. Yang Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline Bioinformatics, April 1, 2008; 24(7): 950 - 957. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 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]
|
|
|
|
 |
|
 F. Cordero, M. Botta, and R. A. Calogero Microarray data analysis and mining approaches Brief Funct Genomic Proteomic, January 22, 2008; (2008) elm034v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. E. Ritchie, J. Silver, A. Oshlack, M. Holmes, D. Diyagama, A. Holloway, and G. K. Smyth A comparison of background correction methods for two-colour microarrays Bioinformatics, October 15, 2007; 23(20): 2700 - 2707. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Kreutz, M.M. B. Rodriguez, T. Maiwald, M. Seidl, H.E. Blum, L. Mohr, and J. Timmer An error model for protein quantification Bioinformatics, October 15, 2007; 23(20): 2747 - 2753. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. D. Storey, J. Y. Dai, and J. T. Leek The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments Biostat., April 1, 2007; 8(2): 414 - 432. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
 |
|
 D. A. Smirnov, B. W. Foulk, G. V. Doyle, M. C. Connelly, L. W.M.M. Terstappen, and S. M. O'Hara Global gene expression profiling of circulating endothelial cells in patients with metastatic carcinomas. Cancer Res., March 15, 2006; 66(6): 2918 - 2922. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Grotkjaer, O. Winther, B. Regenberg, J. Nielsen, and L. K. Hansen Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm Bioinformatics, January 1, 2006; 22(1): 58 - 67. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
|
|
S. Bilke, Q.-R. Chen, C. C. Whiteford, and J. Khan Detection of low level genomic alterations by comparative genomic hybridization based on cDNA micro-arrays Bioinformatics, April 1, 2005; 21(7): 1138 - 1145. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Delmar, S.ép. Robin, and J. J. Daudin VarMixt: efficient variance modelling for the differential analysis of replicated gene expression data Bioinformatics, February 15, 2005; 21(4): 502 - 508. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. K. Lin, D. Chudova, G. W. Hatfield, P. Smyth, and B. Andersen Identification of hair cycle-associated genes from time-course gene expression profile data by using replicate variance PNAS, November 9, 2004; 101(45): 15955 - 15960. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Dozmorov, N. Knowlton, Y. Tang, A. Shields, P. Pathipvanich, J. N. Jarvis, and M. Centola Hypervariable genes--experimental error or hidden dynamics Nucleic Acids Res., October 28, 2004; 32(19): e147 - e147. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Armengaud, R. Breitling, and A. Amtmann The Potassium-Dependent Transcriptome of Arabidopsis Reveals a Prominent Role of Jasmonic Acid in Nutrient Signaling Plant Physiology, September 1, 2004; 136(1): 2556 - 2576. [Abstract] [Full Text] [PDF]
|
|