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Bioinformatics Advance Access published online on March 7, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl068
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received November 10, 2005
Revised February 13, 2006
Accepted February 21, 2006

Article

A calibration method for estimating absolute expression levels from microarray data

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

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

* To whom correspondence should be addressed.
Kathleen Marchal, E-mail: kathleen.marchal{at}biw.kuleuven.be


  Abstract

Motivation: We describe an approach to normalizing 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 data set, 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.

Associate Editor: Joaquin Dopazo
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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]


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