Skip Navigation

This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
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 (49)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Edwards, D.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Edwards, D.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics Vol. 19 no. 7 2003
Pages 825-833
© 2003 Oxford University Press

Non-linear normalization and background correction in one-channel cDNA microarray studies

David Edwards

Department of Biostatistics, Novo Nordisk, Bagsvaerd Denmark

Received on September 9, 2002 ; revised on November 14, 2002 ; accepted on November 15, 2002

Motivation: Data from one-channel cDNA microarray studies may exhibit poor reproducibility due to spatial heterogeneity, non-linear array-to-array variation and problems in correcting for background. Uncorrected, these phenomena can give rise to misleading conclusions.

Results: Spatial heterogeneity may be corrected using two-dimensional loess smoothing (Colantuoni et al., 2002). Non-linear between-array variation may be corrected using an iterative application of one-dimensional loess smoothing. A method for background correction using a smoothing function rather than simple subtraction is described. These techniques promote within-array spatial uniformity and between-array reproducibility. Their application is illustrated using data from a study of the effects of an insulin sensitizer, rosiglitazone, on gene expression in white adipose tissue in diabetic db/db mice. They may also be useful with data from two-channel cDNA microarrays and from oligonucleotide arrays.

Availability: R functions for the methods described are available on request from the author.

Contact: DEd{at}novonordisk.com


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
 Am. J. Physiol. Lung Cell. Mol. Physiol.Home page
M. Cabanski, J. Wilhelm, Z. Zaslona, M. Steinmuller, L. Fink, W. Seeger, and J. Lohmeyer
Genome-wide transcriptional profiling of mononuclear phagocytes recruited to mouse lungs in response to alveolar challenge with the TLR2 agonist Pam3CSK4
Am J Physiol Lung Cell Mol Physiol, October 1, 2009; 297(4): L608 - L618.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Respir. Crit. Care Med.Home page
P. P. Massion, Y. Zou, H. Chen, A. Jiang, P. Coulson, C. I. Amos, X. Wu, I. Wistuba, Q. Wei, Y. Shyr, et al.
Smoking-related Genomic Signatures in Non-Small Cell Lung Cancer
Am. J. Respir. Crit. Care Med., December 1, 2008; 178(11): 1164 - 1172.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
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]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. B. Axelsen, J. Lotem, L. Sachs, and E. Domany
Genes overexpressed in different human solid cancers exhibit different tissue-specific expression profiles
PNAS, August 7, 2007; 104(32): 13122 - 13127.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
S. M. Kristoffersen, S. Ravnum, N. J. Tourasse, O. A. Okstad, A.-B. Kolsto, and W. Davies
Low Concentrations of Bile Salts Induce Stress Responses and Reduce Motility in Bacillus cereus ATCC 14570
J. Bacteriol., July 15, 2007; 189(14): 5302 - 5313.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. Yoon, Y. Yang, J. Choi, and J. Seong
Large scale data mining approach for gene-specific standardization of microarray gene expression data
Bioinformatics, December 1, 2006; 22(23): 2898 - 2904.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
K. Rogasch, V. Ruhmling, J. Pane-Farre, D. Hoper, C. Weinberg, S. Fuchs, M. Schmudde, B. M. Broker, C. Wolz, M. Hecker, et al.
Influence of the Two-Component System SaeRS on Global Gene Expression in Two Different Staphylococcus aureus Strains.
J. Bacteriol., November 1, 2006; 188(22): 7742 - 7758.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
M. J. Allen, T. Forster, D. C. Schroeder, M. Hall, D. Roy, P. Ghazal, and W. H. Wilson
Locus-specific gene expression pattern suggests a unique propagation strategy for a giant algal virus.
J. Virol., August 1, 2006; 80(15): 7699 - 7705.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Rainer, F. Sanchez-Cabo, G. Stocker, A. Sturn, and Z. Trajanoski
CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W498 - W503.
[Abstract] [Full Text] [PDF]

Home page
 DiabetesHome page
M. Hansson, A. Tonning, U. Frandsen, A. Petri, J. Rajagopal, M. C.O. Englund, R. S. Heller, J. Hakansson, J. Fleckner, H. N. Skold, et al.
Artifactual Insulin Release From Differentiated Embryonic Stem Cells
Diabetes, October 1, 2004; 53(10): 2603 - 2609.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
S. I. Meireles, E. B. Cristo, A. F. Carvalho, R. Hirata Jr., A. Pelosof, L. I. Gomes, W. K. Martins, M. D. Begnami, C. Zitron, A. L. Montagnini, et al.
Molecular Classifiers for Gastric Cancer and Nonmalignant Diseases of the Gastric Mucosa
Cancer Res., February 15, 2004; 64(4): 1255 - 1265.
[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.