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Bioinformatics Advance Access published online on November 8, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl550
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received July 23, 2006
Revised October 20, 2006
Accepted October 22, 2006

Article

Inferential, robust non-negative matrix factorization analysis of microarray data

Paul Fogel 1, S. Stanley Young 2 *, Douglas M. Hawkins 3, and Nathalie Ledirac 4

1 Consultant, 4, rue Le Goff, F-75005, Paris, France
2 National Institute of Statistical Sciences, P.O. Box 14006, Research Triangle Park, NC 27709-4006
3 School of Statistics, University of Minnesota, 313 Ford Hall, 224 Church Street NE, Minneapolis, MN 55455
4 Laboratoire de Toxicologie Cellulaire et Moléculaire, Centre de Recherche INRA, 400 Route des Chappes, 06903 Sophia-Antipolis, France

* To whom correspondence should be addressed.
S. Stanley Young, E-mail: young{at}niss.org


  Abstract

Motivation: Modern methods like micro arrays, proteomics and metabolomics often produce data sets where there are many more predictor variables than observations. Research in these areas is often exploratory; even so, there is interest in statistical methods that accurately point to effects that are likely to replicate. Correlations among predictors are used to improve the statistical analysis. We exploit two ideas: non-negative matrix factorization methods that create ordered sets of predictors; and statistical testing within ordered sets which is done sequentially, removing the need for correction for multiple testing within the set.

Results: Simulations and theory point to increased statistical power. Computational algorithms are described in detail. The analysis and biological interpretation of a real data set are given. In addition to the increased power, the benefit of our method is that the organized gene lists are likely to lead better understanding of the biology.

Availablity: A SAS JMP executable script is available from http://www.niss.org/irNMF.

Supplementary Information: http://www.niss.org/irNMF.

Associate Editor: David Rocke
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