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Bioinformatics Advance Access published online on January 31, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti288
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Bioinformatics © Oxford University Press 2005; all rights reserved.
Received October 7, 2004
Revised December 27, 2004
Accepted January 19, 2005

Applications note

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

Sek Won Kong 1*, Kyu-Baek Hwang 2, Richard D. Kim 3, Byoung-Tak Zhang 2, Steven A. Greenberg 4, Isaac S. Kohane 5, and Peter J. Park 5

1 Bauer Center for Genomics Research, Harvard University, Cambridge, MA, USA; Molecular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
2 School of Computer Science and Engineering, Seoul National University, Korea
3 Harvard-Partners Center for Genetics and Genomics, Boston, MA, USA
4 Dept of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Children's Hospital Informatics Program, Boston, MA, USA
5 Harvard-Partners Center for Genetics and Genomics, Boston, MA, USA; Children's Hospital Informatics Program, Boston, MA, USA

* To whom correspondence should be addressed.
Sek Won Kong, E-mail: skong{at}cgr.harvard.edu


  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.


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