Iterative normalization of cDNA microarray data

Yue Wang, Jianping Lu, Richard Lee, Zhiping Gu, Robert Clarke

Research output: Contribution to journalArticlepeer-review

45 Scopus citations

Abstract

This paper describes a new approach to normalizing microarray expression data. The novel feature is to unify the tasks of estimating normalization coefficients and identifying control gene set. Unification is realized by constructing a window function over the scatter plot defining the subset of constantly expressed genes and by affecting optimization using an iterative procedure. The structure of window function gates contributions to the control gene set used to estimate normalization coefficients. This window measures the consistency of the matched neighborhoods in the scatter plot and provides a means of rejecting control gene outliers. The recovery of normalizational regression and control gene selection are interleaved and are realized by applying coupled operations to the mean square error function. In this way, the two processes bootstrap one another. We evaluate the technique on real microarray data from breast cancer cell lines and complement the experiment with a data cluster visualization study.

Original languageEnglish (US)
Pages (from-to)29-37
Number of pages9
JournalIEEE Transactions on Information Technology in Biomedicine
Volume6
Issue number1
DOIs
StatePublished - Mar 2002
Externally publishedYes

Keywords

  • Data normalization
  • Dynamic programming
  • Gene expression
  • Gene microarray
  • Linear regression

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