Pvclust: an R package for assessing the uncertainty in hierarchical clustering
- PMID: 16595560
- DOI: 10.1093/bioinformatics/btl117
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.
Similar articles
-
Multi-way clustering of microarray data using probabilistic sparse matrix factorization.Bioinformatics. 2005 Jun;21 Suppl 1:i144-51. doi: 10.1093/bioinformatics/bti1041. Bioinformatics. 2005. PMID: 15961451
-
ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles.Bioinformatics. 2006 Jun 15;22(12):1538-9. doi: 10.1093/bioinformatics/btl129. Epub 2006 Apr 10. Bioinformatics. 2006. PMID: 16606685
-
AnovArray: a set of SAS macros for the analysis of variance of gene expression data.BMC Bioinformatics. 2005 Jun 16;6:150. doi: 10.1186/1471-2105-6-150. BMC Bioinformatics. 2005. PMID: 15960854 Free PMC article.
-
Microarray data analysis: from disarray to consolidation and consensus.Nat Rev Genet. 2006 Jan;7(1):55-65. doi: 10.1038/nrg1749. Nat Rev Genet. 2006. PMID: 16369572 Review.
-
Comparing algorithms for clustering of expression data: how to assess gene clusters.Methods Mol Biol. 2009;541:479-509. doi: 10.1007/978-1-59745-243-4_21. Methods Mol Biol. 2009. PMID: 19381534 Review.
Cited by
-
Embryonic mammary signature subsets are activated in Brca1-/- and basal-like breast cancers.Breast Cancer Res. 2013 Mar 18;15(2):R25. doi: 10.1186/bcr3403. Breast Cancer Res. 2013. PMID: 23506684 Free PMC article.
-
RNA-seq analysis reveals significant transcriptome changes in turbot (Scophthalmus maximus) suffering severe enteromyxosis.BMC Genomics. 2014 Dec 19;15:1149. doi: 10.1186/1471-2164-15-1149. BMC Genomics. 2014. PMID: 25526753 Free PMC article.
-
Bioinformatic analysis linking genomic defects to chemosensitivity and mechanism of action.PLoS One. 2021 Apr 28;16(4):e0243336. doi: 10.1371/journal.pone.0243336. eCollection 2021. PLoS One. 2021. PMID: 33909629 Free PMC article.
-
Exome sequencing reveals pathogenic mutations in 91 strains of mice with Mendelian disorders.Genome Res. 2015 Jul;25(7):948-57. doi: 10.1101/gr.186882.114. Epub 2015 Apr 27. Genome Res. 2015. PMID: 25917818 Free PMC article.
-
Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes.Elife. 2020 Jun 17;9:e56998. doi: 10.7554/eLife.56998. Elife. 2020. PMID: 32553109 Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
Other Literature Sources
