Normalization of single-channel DNA array data by principal component analysis

Radka Stoyanova, Troy D. Querec, Truman R. Brown, Christos Patriotis

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

Motivation: Detailed comparison and analysis of the output of DNA gene expression arrays from multiple samples require global normalization of the measured individual gene intensities from the different hybridizations. This is needed for accounting for variations in array preparation and sample hybridization conditions. Results: Here, we present a simple, robust and accurate procedure for the global normalization of datasets generated with single-channel DNA arrays based on principal component analysis. The procedure makes minimal assumptions about the data and performs well in cases where other standard procedures produced biased estimates. It is also insensitive to data transformation, filtering (thresholding) and pre-screening.

Original languageEnglish
Pages (from-to)1772-1784
Number of pages13
JournalBioinformatics
Volume20
Issue number11
DOIs
StatePublished - Jul 22 2004
Externally publishedYes

Fingerprint

Principal Component Analysis
Oligonucleotide Array Sequence Analysis
Principal component analysis
Normalization
DNA
Gene expression
Data Transformation
Screening
Genes
Thresholding
Gene Expression
Biased
Preparation
Filtering
Gene
Output
Estimate

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

Cite this

Normalization of single-channel DNA array data by principal component analysis. / Stoyanova, Radka; Querec, Troy D.; Brown, Truman R.; Patriotis, Christos.

In: Bioinformatics, Vol. 20, No. 11, 22.07.2004, p. 1772-1784.

Research output: Contribution to journalArticle

Stoyanova, Radka ; Querec, Troy D. ; Brown, Truman R. ; Patriotis, Christos. / Normalization of single-channel DNA array data by principal component analysis. In: Bioinformatics. 2004 ; Vol. 20, No. 11. pp. 1772-1784.
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