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Briefings in Bioinformatics Advance Access originally published online on December 5, 2007
Briefings in Bioinformatics 2008 9(1):25-33; doi:10.1093/bib/bbm055
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© The Author 2007. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

An overview of image-processing methods for Affymetrix GeneChips

Jose M. Arteaga-Salas a, Harry Zuzan a, William B. Langdon, Graham J. G. Upton and Andrew P. Harrison

Corresponding author: Andrew P. Harrison, Department of Mathematical Sciences, University of Essex, Wivenhoe Park, Colchester, UK, CO4 3SQ. Tel: +44 1206 872964; Fax: +44 1206 873043; E-mail: harry{at}essex.ac.uk

We present an overview of image-processing methods for Affymetrix GeneChips. All GeneChips are affected to some extent by spatially coherent defects and image processing has a number of potential impacts on the downstream analysis of GeneChip data. Fortunately, there are now a number of robust and accurate algorithms, which identify the most disabling defects. One group of algorithms concentrate on the transformation from the original hybridisation DAT image to the representative CEL file. Another set uses dedicated pattern recognition routines to detect different types of hybridisation defect in replicates. A third type exploits the information provided by public repositories of GeneChips (such as GEO). The use of these algorithms improves the sensitivity of GeneChips, and should be a prerequisite for studies in which there are only few probes per relevant biological signal, such as exon arrays and SNP chips.

Keywords: Affymetrix microarrays, image processing

aThe first two authors contributed equally to this work.

Submitted: August 28, 2007. Received (in revised form): October 12, 2007.


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