Skip Navigation



Bioinformatics Advance Access published online on May 27, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth327
Bioinformatics © Oxford University Press 2004; all rights reserved
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
20/16/2778    most recent
bth327v1
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 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 arrowRequest Permissions
Google Scholar
Right arrow Articles by Ballman, K. V.
Right arrow Articles by Therneau, T. M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Ballman, K. V.
Right arrow Articles by Therneau, T. M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Received January 9, 2004
Accepted February 20, 2004

Article

Faster cyclic loess: normalizing DNA arrays via linear models

Karla V. Ballman 1*, Diane E. Grill 1, Ann L. Oberg 1, Terry M. Therneau 1

1 Division of Biostatistics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA

* To whom correspondence should be addressed. E-mail: ballman{at}mayo.edu.


  Abstract

Motivation: Our goal was to develop a normalization technique that yields results similar to cyclic loess normalization and with speed comparable to quantile normalization.

Results: Fastlo yields normalized values similar to cyclic loess and quantile normalization and is fast; it is at least an order of magnitude faster than cyclic loess and approaches the speed of quantile normalization. Furthermore, fastlo is more versatile than both cyclic loess and quantile normalization because it is model-based.

Availability: The Splus function for fastlo normalization is available from the authors.


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
 Mol. Endocrinol.Home page
H. V. Heemers, K. M. Regan, L. J. Schmidt, S. K. Anderson, K. V. Ballman, and D. J. Tindall
Androgen Modulation of Coregulator Expression in Prostate Cancer Cells
Mol. Endocrinol., April 1, 2009; 23(4): 572 - 583.
[Abstract] [Full Text] [PDF]

Home page
 BrainHome page
J. Fassunke, M. Majores, A. Tresch, P. Niehusmann, A. Grote, S. Schoch, and A. J. Becker
Array analysis of epilepsy-associated gangliogliomas reveals expression patterns related to aberrant development of neuronal precursors
Brain, November 1, 2008; 131(11): 3034 - 3050.
[Abstract] [Full Text] [PDF]

Home page
 CirculationHome page
K. V. Ballman
Genetics and Genomics: Gene Expression Microarrays
Circulation, October 7, 2008; 118(15): 1593 - 1597.
[Full Text] [PDF]

Home page
 Cancer Res.Home page
A. K. McCollum, C. J. TenEyck, B. Stensgard, B. W. Morlan, K. V. Ballman, R. B. Jenkins, D. O. Toft, and C. Erlichman
P-Glycoprotein-Mediated Resistance to Hsp90-Directed Therapy Is Eclipsed by the Heat Shock Response
Cancer Res., September 15, 2008; 68(18): 7419 - 7427.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
L. Li, B. Fridley, K. Kalari, G. Jenkins, A. Batzler, S. Safgren, M. Hildebrandt, M. Ames, D. Schaid, and L. Wang
Gemcitabine and Cytosine Arabinoside Cytotoxicity: Association with Lymphoblastoid Cell Expression
Cancer Res., September 1, 2008; 68(17): 7050 - 7058.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
A. M. Moyer, O. E. Salavaggione, T.-Y. Wu, I. Moon, B. W. Eckloff, M. A.T. Hildebrandt, D. J. Schaid, E. D. Wieben, and R. M. Weinshilboum
Glutathione S-Transferase P1: Gene Sequence Variation and Functional Genomic Studies
Cancer Res., June 15, 2008; 68(12): 4791 - 4801.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
A. M. Moyer, O. E. Salavaggione, S. J. Hebbring, I. Moon, M. A.T. Hildebrandt, B. W. Eckloff, D. J. Schaid, E. D. Wieben, and R. M. Weinshilboum
Glutathione S-Transferase T1 and M1: Gene Sequence Variation and Functional Genomics
Clin. Cancer Res., December 1, 2007; 13(23): 7207 - 7216.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
A. L. Oberg, D. W. Mahoney, K. V. Ballman, and T. M. Therneau
Joint estimation of calibration and expression for high-density oligonucleotide arrays
Bioinformatics, October 1, 2006; 22(19): 2381 - 2387.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
T. Enver, S. Soneji, C. Joshi, J. Brown, F. Iborra, T. Orntoft, T. Thykjaer, E. Maltby, K. Smith, R. A. Dawud, et al.
Cellular differentiation hierarchies in normal and culture-adapted human embryonic stem cells
Hum. Mol. Genet., November 1, 2005; 14(21): 3129 - 3140.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. E. Eckel, C. Gennings, T. M. Therneau, L. D. Burgoon, D. R. Boverhof, and T. R. Zacharewski
Normalization of two-channel microarray experiments: a semiparametric approach
Bioinformatics, April 1, 2005; 21(7): 1078 - 1083.
[Abstract] [Full Text] [PDF]

Home page
 BloodHome page
R. S. Abraham, K. V. Ballman, A. Dispenzieri, D. E. Grill, M. K. Manske, T. L. Price-Troska, N. G. Paz, M. A. Gertz, and R. Fonseca
Functional gene expression analysis of clonal plasma cells identifies a unique molecular profile for light chain amyloidosis
Blood, January 15, 2005; 105(2): 794 - 803.
[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.