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Title A Calibration Method for Estimating Absolute Expression Levels from Microarray Data R.pdf

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Title A Calibration Method for Estimating Absolute Expression Levels from Microarray Data R

1Title: A Calibration Method for Estimating Absolute Expression Levels from Microarray Data Running head: A Calibration Method for Microarray Data Authors: Kristof Engelen1, Bart Naudts2, Bart De Moor1, Kathleen Marchal*3,1 Author affiliations: 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 Corresponding author*: Kathleen Marchal Kasteelpark Arenberg 20 B-3001 Leuven Belgium Telephone: +3216329685, Fax: +3216321966 E-mail: kathleen.marchal@biw.kuleuven.be Keywords: microarrays, external controls, spikes, normalization, calibration ? The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org Associate Editor: Joaquin Dopazo Bioinformatics Advance Access published March 7, 2006 2Abstract 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.