Article

Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data

  1. Eric E. Schadt1,4,*,
  2. Cheng Li3,
  3. Byron Ellis2,
  4. Wing H. Wong2,3,*

Article first published online: 29 JAN 2002

DOI: 10.1002/jcb.10073

Issue

Journal of Cellular Biochemistry

Journal of Cellular Biochemistry

Supplement: Enhancing Drug Discovery and Development

Volume 84, Issue Supplement 37, pages 120–125, 2001

Additional Information

How to Cite

Schadt, E. E., Li, C., Ellis, B. and Wong, W. H. (2001), Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. J. Cell. Biochem., 84: 120–125. doi: 10.1002/jcb.10073

Author Information

  1. 1

    Department of Biomathematics, University of California, Los Angeles, California

  2. 2

    Department of Statistics, Harvard University, Cambridge, Massachusetts

  3. 3

    Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts

  4. 4

    Departments of Informatics, Rosetta Inpharmatics, Kirkland, Washington

*Department of Biomathematics, University of California, Los Angeles, CA and Departments of Informatics, Rosetta Inpharmatics, Kirkland, WA.

Publication History

  1. Issue published online: 29 JAN 2002
  2. Article first published online: 29 JAN 2002
  3. Manuscript Accepted: 22 AUG 2001
  4. Manuscript Received: 21 AUG 2001

Funded by

  • NSF. Grant Numbers: DMS-9703918, DBI-9904701

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Keywords:

  • feature extraction;
  • normalization;
  • oligonucleotide array;
  • gene expression

Abstract

Algorithms for performing feature extraction and normalization on high-density oligonucleotide gene expression arrays, have not been fully explored, and the impact these algorithms have on the downstream analysis is not well understood. Advances in such low-level analysis methods are essential to increase the sensitivity and specificity of detecting whether genes are present and/or differentially expressed. We have developed and implemented a number of algorithms for the analysis of expression array data in a software application, the DNA-Chip Analyzer (dChip). In this report, we describe the algorithms for feature extraction and normalization, and present validation data and comparison results with some of the algorithms currently in use. J. Cell. Biochem. Suppl. 37: 120–125, 2001. © 2002 Wiley-Liss, Inc.

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