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Open Access Highly Accessed Methodology article

A novel approach to the clustering of microarray data via nonparametric density estimation

Riccardo De Bin and Davide Risso*

Author Affiliations

Department of Statistical Sciences, University of Padova, Padova, Italy

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BMC Bioinformatics 2011, 12:49  doi:10.1186/1471-2105-12-49

Published: 8 February 2011

Abstract

Background

Cluster analysis is a crucial tool in several biological and medical studies dealing with microarray data. Such studies pose challenging statistical problems due to dimensionality issues, since the number of variables can be much higher than the number of observations.

Results

Here, we present a general framework to deal with the clustering of microarray data, based on a three-step procedure: (i) gene filtering; (ii) dimensionality reduction; (iii) clustering of observations in the reduced space. Via a nonparametric model-based clustering approach we obtain promising results both in simulated and real data.

Conclusions

The proposed algorithm is a simple and effective tool for the clustering of microarray data, in an unsupervised setting.