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Biostatistics Advance Access originally published online on August 24, 2006
Biostatistics 2007 8(2):433-437; doi:10.1093/biostatistics/kxl020
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© The Author 2006. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org.

FGX: a frequentist gene expression index for Affymetrix arrays

Vilda Purutçuoglu and Ernst Wit*

Department of Mathematics and Statistics, Lancaster University, Lancaster, LA1 4YF, UK e.wit{at}lancaster.ac.uk

* To whom correspondence should be addressed.

We consider a new frequentist gene expression index for Affymetrix oligonucleotide DNA arrays, using a similar probe intensity model as suggested by Hein and others (2005), called the Bayesian gene expression index (BGX). According to this model, the perfect match and mismatch values are assumed to be correlated as a result of sharing a common gene expression signal. Rather than a Bayesian approach, we develop a maximum likelihood algorithm for estimating the underlying common signal. In this way, estimation is explicit and much faster than the BGX implementation. The observed Fisher information matrix, rather than a posterior credibility interval, gives an idea of the accuracy of the estimators. We evaluate our method using benchmark spike-in data sets from Affymetrix and GeneLogic by analyzing the relationship between estimated signal and concentration, i.e. true signal, and compare our results with other commonly used methods.

Keywords: Affymetrix; Fisher information matrix; GeneChip; Gene expression; Maximum likelihood; Probe-level analysis; Spike-in data sets

Received April 13, 2006; revised July 6, 2006; accepted for publication August 2, 2006.


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