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Bioinformatics Advance Access originally published online on March 7, 2006
Bioinformatics 2006 22(10):1251-1258; 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

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

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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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