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Bioinformatics Advance Access originally published online on September 13, 2005
Bioinformatics 2005 21(22):4162-4168; doi:10.1093/bioinformatics/bti668
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

Oligonucleotide arrays: information from replication and spatial structure

Graham J. G. Upton 1,* and Julie C. Lloyd 2

1Department of Mathematical Sciences, University of Essex Colchester, Essex CO4 3SQ, UK
2Department of Biological Sciences, University of Essex Colchester, Essex CO4 3SQ, UK

*To whom correspondence should be addressed.

Motivation: The introduction of oligonucleotide DNA arrays has resulted in much debate concerning appropriate models for the measurement of gene expression. By contrast, little account has been taken of the possibility of identifying the physical imperfections in the raw data.

Results: This paper demonstrates that, with the use of replicates and an awareness of the spatial structure, deficiencies in the data can be identified, the possibility of their correction can be ascertained and correction can be effected (by use of local scaling) where possible. The procedures were motivated by data from replicates of Arabidopsis thaliana using the GeneChip® ATH1-121501 microarray. Similar problems are illustrated for GeneChip® Human Genome U133 arrays and for the newer and larger GeneChip® Wheat Genome microarray.

Availability: R code is freely available on request.

Contact: gupton{at}essex.ac.uk

Received on January 30, 2005; revised on August 29, 2005; accepted on September 6, 2005

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