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Nucleic Acids Research, 2003, Vol. 31, No. 7 1962-1968
© 2003 Oxford University Press

Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays

Doeke Hekstra, Alexander R. Taussig, Marcelo Magnasco and Felix Naef

Center for Studies in Physics and Biology, Laboratory of Mathematical Physics, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA

*To whom correspondence should be addressed. Tel: +1 212 327 8186; Fax: +1 212 327 7422; Email: felix{at}funes.rockefeller.edu

Oligonucleotide microarrays are based on the hybridization of labeled mRNA molecules to short length oligonucleotide probes on a glass surface. Two effects have been shown to affect the raw data: the sequence dependence of the probe hybridization properties and the chemical saturation resulting from surface adsorption processes. We address both issues simultaneously using a physically motivated hybridization model. Based on publicly available calibration data sets, we show that Langmuir adsorption accurately describes GeneChip hybridization, with model parameters that we predict from the sequence composition of the probes. Because these parameters have physical units, we are able to estimate absolute mRNA concentrations in picomolar. Additionally, by accounting for chemical saturation, we substantially reduce the compressive bias of differential expression estimates that normally occurs toward high concentrations.


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