Get access

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

Authors

  • Eric E. Schadt,

    Corresponding author
    1. Department of Biomathematics, University of California, Los Angeles, California
    2. Departments of Informatics, Rosetta Inpharmatics, Kirkland, Washington
    • Department of Biomathematics, University of California, Los Angeles, CA and Departments of Informatics, Rosetta Inpharmatics, Kirkland, WA.
    Search for more papers by this author
  • Cheng Li,

    1. Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts
    Search for more papers by this author
  • Byron Ellis,

    1. Department of Statistics, Harvard University, Cambridge, Massachusetts
    Search for more papers by this author
  • Wing H. Wong

    Corresponding author
    1. Department of Statistics, Harvard University, Cambridge, Massachusetts
    2. Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts
    • Departments of Biostatistics, Harvard School of Public Health, 655 Hungtington, Ave, Boston, MA.
    Search for more papers by this author

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.

Get access to the full text of this article

Ancillary