Skip Navigation


Bioinformatics Advance Access originally published online on March 7, 2006
Bioinformatics 2006 22(10):1251-1258; doi:10.1093/bioinformatics/btl068
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow Supplementary Data
Right arrow All Versions of this Article:
22/10/1251    most recent
btl068v1
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 (3)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Engelen, K.
Right arrow Articles by Marchal, K.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Engelen, K.
Right arrow Articles by Marchal, K.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

A calibration method for estimating absolute expression levels from microarray data

Kristof Engelen 1, Bart Naudts 2, Bart De Moor 1 and Kathleen Marchal 1,3,*

1 BIOI@SCD, Department of Electrical Engineering K.U.Leuven, Kasteelpark Arenberg 10, B-3001 Leuven, Belgium
2 ISLab, Department of Mathematics and Computer Science, University of Antwerp Middelheimlaan 1, B-2020 Antwerpen, Belgium
3 CMPG, Department of Microbial and Molecular Systems K.U.Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium

*To whom correspondence should be addressed.

Motivation: We describe an approach to normalize spotted microarray data, based on a physically motivated calibration model. This model consists of two major components, describing the hybridization of target transcripts to their corresponding probes on the one hand, and the measurement of fluorescence from the hybridized, labeled target on the other hand. The model parameters and error distributions are estimated from external control spikes.

Results: Using a publicly available dataset, we show that our procedure is capable of adequately removing the typical non-linearities of the data, without making any assumptions on the distribution of differences in gene expression from one biological sample to the next. Since our model links target concentration to measured intensity, we show how absolute expression values of target transcripts in the hybridization solution can be estimated up to a certain degree.

Contact: kathleen.marchal{at}biw.kuleuven.be

Supplementary information: Supplementary data are available at Bioinformatics online.

Received on November 10, 2005; revised on February 13, 2006; accepted on February 21, 2006

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. Zhao, K. Engelen, B. De Moor, and K. Marchal
CALIB: a Bioconductor package for estimating absolute expression levels from two-color microarray data
Bioinformatics, July 1, 2007; 23(13): 1700 - 1701.
[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.