Cluster Analysis of Genomic Data

Abstract

We provide an overview of existing partitioning and hierarchical clustering algorithms in R. We discuss statistical issues and methods in choosing the number of clusters, the choice of clustering algorithm, and the choice of dissimilarity matrix. We also show how to visualize a clustering result by plotting ordered dissimilarity matrices in R. A new R package hopach, which implements the Hierarchical Ordered Partitioning And Collapsing Hybrid (HOPACH) algorithm, is presented (van der Laan and Pollard, 2003). The methodology is applied to a renal cell cancer gene expression data set.