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Bioinformatics. 2001 Apr;17(4):309-18.

Validating clustering for gene expression data.

Author information

  • 1Computer Science and Engineering, Box 352350, University of Washington, Seattle, WA 98195, USA.

Abstract

MOTIVATION:

Many clustering algorithms have been proposed for the analysis of gene expression data, but little guidance is available to help choose among them. We provide a systematic framework for assessing the results of clustering algorithms. Clustering algorithms attempt to partition the genes into groups exhibiting similar patterns of variation in expression level. Our methodology is to apply a clustering algorithm to the data from all but one experimental condition. The remaining condition is used to assess the predictive power of the resulting clusters-meaningful clusters should exhibit less variation in the remaining condition than clusters formed by chance.

RESULTS:

We successfully applied our methodology to compare six clustering algorithms on four gene expression data sets. We found our quantitative measures of cluster quality to be positively correlated with external standards of cluster quality.

PMID:
11301299
[PubMed - indexed for MEDLINE]
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