Cluster Analysis of Genomic Data [chapter]

K. S. Pollard, M. J. van der Laan
2005 Bioinformatics and Computational Biology Solutions Using R and Bioconductor  
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
more » ... llard, 2003). The methodology is applied to a renal cell cancer gene expression data set.
doi:10.1007/0-387-29362-0_13 fatcat:4hgk6snaevhhxjysdbihr37tci