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An Overview of Clustering Applied to Molecular Biology

  • Rebecca Nugent
  • Marina Meila
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 620)

Abstract

In molecular biology, we are often interested in determining the group structure in, e.g., a population of cells or microarray gene expression data. Clustering methods identify groups of similar observations, but the results can depend on the chosen method’s assumptions and starting parameter values. In this chapter, we give a broad overview of both attribute- and similarity-based clustering, describing both the methods and their performance. The parametric and nonparametric approaches presented vary in whether or not they require knowing the number of clusters in advance as well as the shapes of the estimated clusters. Additionally, we include a biclustering algorithm that incorporates variable selection into the clustering procedure. We finish with a discussion of some common methods for comparing two clustering solutions (possibly from different methods). The user is advised to devote time and attention to determining the appropriate clustering approach (and any corresponding parameter values) for the specific application prior to analysis.

Key words

Cluster analysis K-means model-based clustering EM algorithm similarity-based clustering spectral clustering nonparametric clustering hierarchical clustering biclustering comparing partitions 

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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Rebecca Nugent
    • 1
  • Marina Meila
    • 2
  1. 1.Department of StatisticsCarnegie Mellon UniversityPittsburghUSA
  2. 2.Department of StatisticsUniversity of WashingtonSeattleUSA

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