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The Scientific World Journal
Volume 2012, Article ID 380495, 11 pages
http://dx.doi.org/10.1100/2012/380495
Research Article

Gene Expression Profiles for Predicting Metastasis in Breast Cancer: A Cross-Study Comparison of Classification Methods

1Research Unit of Human Genetics, Institute of Clinical Research, University of Southern Denmark, Sdr. Boulevard 29, 5000 Odense C, Denmark
2Department of Clinical Genetics, Odense University Hospital, Sdr. Boulevard 29, 5000 Odense C, Denmark
3Institute of Public Health, University of Southern Denmark, J. B. Winsløws Vej 9B, 5000 Odense C, Denmark

Received 25 August 2012; Accepted 2 October 2012

Academic Editors: M. A. Kon and K. Najarian

Copyright © 2012 Mark Burton et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Machine learning has increasingly been used with microarray gene expression data and for the development of classifiers using a variety of methods. However, method comparisons in cross-study datasets are very scarce. This study compares the performance of seven classification methods and the effect of voting for predicting metastasis outcome in breast cancer patients, in three situations: within the same dataset or across datasets on similar or dissimilar microarray platforms. Combining classification results from seven classifiers into one voting decision performed significantly better during internal validation as well as external validation in similar microarray platforms than the underlying classification methods. When validating between different microarray platforms, random forest, another voting-based method, proved to be the best performing method. We conclude that voting based classifiers provided an advantage with respect to classifying metastasis outcome in breast cancer patients.