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

Bioinformatics. 2005 May 1;21(9):2116-7. doi: 10.1093/bioinformatics/bti288. Epub 2005 Jan 31.

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

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms*
  • DNA Probes / genetics*
  • Gene Expression Profiling / instrumentation
  • Gene Expression Profiling / methods*
  • Information Storage and Retrieval / methods
  • Oligonucleotide Array Sequence Analysis / instrumentation
  • Oligonucleotide Array Sequence Analysis / methods*
  • Sequence Alignment / instrumentation
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA / instrumentation
  • Sequence Analysis, DNA / methods*
  • Software*

Substances

  • DNA Probes