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Bioinformatics Advance Access originally published online on April 4, 2006
Bioinformatics 2006 22(12):1540-1542; doi:10.1093/bioinformatics/btl117
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Pvclust: an R package for assessing the uncertainty in hierarchical clustering

Ryota Suzuki 1,2,* and Hidetoshi Shimodaira 1

1 Department of Mathematical and Computing Sciences, Tokyo Institute of Technology 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8552, Japan
2 Ef-prime, Inc. 2-17-5 Nihonbashi-Kayabacho, Chuo-ku, Tokyo 103-0025, Japan

*To whom correspondence should be addressed.

Summary: 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.

Availability: The program is freely distributed under GNU General Public License (GPL) and can directly be installed from CRAN (http://cran.r-project.org/), the official R package archive. The instruction and program source code are available at http://www.is.titech.ac.jp/~shimo/prog/pvclust

Contact: ryota.suzuki{at}is.titech.ac.jp

Received on August 30, 2005; revised on March 6, 2006; accepted on March 25, 2006

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