title: Pvclust: an R package for assessing the uncertainty in hierarchical clustering.
abstract: Pvclust is an add-on package for a statistical software R to assess the uncertainty in hierarchical cluster analysis. Pvclust can be used easily for general statistical problems, such as DNA microarray analysis, to perform the bootstrap analysis of clustering, which has been popular in phylogenetic analysis. Pvclust calculates probability values (p-values) for each cluster using bootstrap resampling techniques. Two types of p-values are available: approximately unbiased (AU) p-value and bootstrap probability (BP) value. Multiscale bootstrap resampling is used for the calculation of AU p-value, which has superiority in bias over BP value calculated by the ordinary bootstrap resampling. In addition the computation time can be enormously decreased with parallel computing option.
authors.affiliation: Department of Mathematical and Computing Sciences, Tokyo Institute of Technology 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8552, Japan. ryota.suzuki@is.titech.ac.jp
authors.forename: Ryota
authors.initials: R
authors.lastname: Suzuki
authors.forename: Hidetoshi
authors.initials: H
authors.lastname: Shimodaira
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D020407:Internet; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011336:Probability; D011381:Programming Languages; D012984:Software; D035501:Uncertainty