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An overview of image-processing methods for Affymetrix GeneChips

Arteaga-Salas, JM and Zuzan, H and Langdon, WB and Upton, GJG and Harrison, AP (2008) 'An overview of image-processing methods for Affymetrix GeneChips.' Briefings in Bioinformatics, 9 (1). pp. 25-33. ISSN 1467-5463

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Abstract

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. © The Author 2007. Published by Oxford University Press.

Item Type: Article
Uncontrolled Keywords: Image Interpretation, Computer-Assisted; Microscopy, Fluorescence, Multiphoton; Image Enhancement; Oligonucleotide Array Sequence Analysis; In Situ Hybridization, Fluorescence; Gene Expression Profiling; Algorithms
Subjects: Q Science > QA Mathematics
Q Science > QH Natural history > QH426 Genetics
Divisions: Faculty of Science and Health
Faculty of Science and Health > Mathematical Sciences, Department of
SWORD Depositor: Elements
Depositing User: Elements
Date Deposited: 04 Oct 2011 13:47
Last Modified: 15 Jan 2022 00:45
URI: http://repository.essex.ac.uk/id/eprint/833

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