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Publication Detail
An overview of image-processing methods for Affymetrix GeneChips
  • Publication Type:
    Journal article
  • Publication Sub Type:
    article
  • Authors:
    Arteaga-Salas JM, Zuzan H, Langdon WB, Upton GJG, Harrison AP
  • Publication date:
    2008
  • Pagination:
    25, 33
  • Journal:
    Briefings in Bioinformatics
  • Volume:
    9
  • Article number:
    1
  • Notes:
    keywords: Affymetrix microarrays, Image processing size: 13 pages
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 concentrates on the transformation from the original hybridisation DAT image to the representative CEL file, while another type uses dedicated pattern recognition routines to detect different types of hybridisation defect in replicates, and 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.
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