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Bioinformatics Vol. 19 no. 2 2003
Pages 178-184
© 2003 Oxford University Press

A study of accuracy and precision in oligonucleotide arrays: extracting more signal at large concentrations

Felix Naef 1,*, Nicholas D. Socci 2 and Marcelo Magnasco 1

1 Center for Studies in Physics and Biology
2 Laboratory for Molecular Genetics, Rockefeller University, 1230 York Avenue, NY 10021, USA

Received on March 8, 2002 ; revised on July 11, 2002 ; accepted on August 20, 2002

Motivation: Despite the success and popularity of oligonucleotide arrays as a high-throughput technique for measuring mRNA expression levels, quantitative calibration studies have until now been limited. The main reason is that suitable data was not available. However, calibration data recently produced by Affymetrix now permits detailed studies of the intensity dependent sensitivity. Given a certain transcript concentration, it is of particular interest to know whether current analysis methods are capable of detecting differential expression ratios of 2 or higher.

Results: Using the calibration data, we demonstrate that while current techniques are capable of detecting changes in the low to mid concentration range, the situation is noticeably worse for high concentrations. In this regime, expression changes as large as 4 fold are severely biased, and changes of 2 are often undetectable. Such effects are mainly the consequence of the sequence specific binding properties of probes, and not the result of optical saturation in the fluorescence measurements. GeneChips are manufactured such that each transcript is probed by a set of sequences with a wide affinity range. We show that this property can be used to design a method capable of reducing the high intensity bias. The idea behind our methods is to transfer the weight of a measurement to a subset of probes with optimal linear response at a given concentration, which can be achieved using local embedding techniques.

Availability: Program source code will be sent electronically upon request.

Contact: felix{at}funes.rockefeller.edu

* To whom correspondence should be addressed.


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