CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays

  • Authors:

  • Sek Won Kong;Kyu-Baek Hwang;Richard D. Kim;Byoung-Tak Zhang;Steven A. Greenberg;Isaac S. Kohane;Peter J. Park

  • Affiliations:

  • Bauer Center for Genomics Research, Harvard University Cambridge, MA, USA;School of Computer Science and Engineering, Seoul National University Korea;Harvard-Partners Center for Genetics and Genomics Boston, MA, USA;School of Computer Science and Engineering, Seoul National University Korea;Department of Neurology, Brigham and Women's Hospital Boston, MA, USA;Harvard-Partners Center for Genetics and Genomics Boston, MA, USA;Harvard-Partners Center for Genetics and Genomics Boston, MA, USA

  • Venue:
  • Bioinformatics
  • Year:
  • 2005

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Abstract

Summary: To increase compatibility between different generations of Affymetrix GeneChip arrays, we propose a method of filtering probes based on their sequences. Our method is implemented as a web-based service for downloading necessary materials for converting the raw data files (*.CEL) for comparative analysis. The user can specify the appropriate level of filtering by setting the criteria for the minimum overlap length between probe sequences and the minimum number of usable probe pairs per probe set. Our website supports a within-species comparison for human and mouse GeneChip arrays. Availability: http://www.crosschip.org Contact: skong@cgr.harvard.edu