Abstract
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.Full text links
Read article at publisher's site: https://doi.org/10.1093/bioinformatics/btl117
Read article for free, from open access legal sources, via Unpaywall:
https://academic.oup.com/bioinformatics/article-pdf/22/12/1540/48837936/bioinformatics_22_12_1540.pdf
References
Articles referenced by this article (7)
Bootstrap confidence levels for phylogenetic trees.
Proc Natl Acad Sci U S A, (23):13429-13434 1996
MED: 8917608
CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP.
Evolution, (4):783-791 1985
MED: 28561359
Diversity of gene expression in adenocarcinoma of the lung.
Proc Natl Acad Sci U S A, (24):13784-13789 2001
MED: 11707590
Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments.
Proc Natl Acad Sci U S A, (16):8961-8965 2001
MED: 11470909
CONSEL: for assessing the confidence of phylogenetic tree selection.
Bioinformatics, (12):1246-1247 2001
MED: 11751242
An approximately unbiased test of phylogenetic tree selection.
Syst Biol, (3):492-508 2002
MED: 12079646
Title not supplied
ANN STAT 2004
Citations & impact
Impact metrics
Citations of article over time
Alternative metrics
Smart citations by scite.ai
Explore citation contexts and check if this article has been
supported or disputed.
https://scite.ai/reports/10.1093/bioinformatics/btl117
Article citations
Diversity, composition and potential roles of sedimentary microbial communities in different coastal substrates around subtropical Okinawa Island, Japan.
Environ Microbiome, 19(1):54, 30 Jul 2024
Cited by: 0 articles | PMID: 39080706 | PMCID: PMC11290285
Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake.
Microbiome, 12(1):133, 20 Jul 2024
Cited by: 0 articles | PMID: 39030632 | PMCID: PMC11265017
Mutations in glioblastoma proteins do not disrupt epitope presentation and recognition, maintaining a specific CD8 T cell immune response potential.
Sci Rep, 14(1):16721, 19 Jul 2024
Cited by: 0 articles | PMID: 39030304 | PMCID: PMC11271619
Single-cell resolution characterization of myeloid-derived cell states with implication in cancer outcome.
Nat Commun, 15(1):5694, 07 Jul 2024
Cited by: 0 articles | PMID: 38972873 | PMCID: PMC11228020
Transcriptional immune suppression and up-regulation of double-stranded DNA damage and repair repertoires in ecDNA-containing tumors.
Elife, 12:RP88895, 19 Jun 2024
Cited by: 1 article | PMID: 38896472 | PMCID: PMC11186631
Go to all (1,214) article citations
Similar Articles
To arrive at the top five similar articles we use a word-weighted algorithm to compare words from the Title and Abstract of each citation.
Multi-way clustering of microarray data using probabilistic sparse matrix factorization.
Bioinformatics, 21 Suppl 1:i144-51, 01 Jun 2005
Cited by: 22 articles | PMID: 15961451
ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles.
Bioinformatics, 22(12):1538-1539, 10 Apr 2006
Cited by: 6 articles | PMID: 16606685
AnovArray: a set of SAS macros for the analysis of variance of gene expression data.
BMC Bioinformatics, 6:150, 16 Jun 2005
Cited by: 5 articles | PMID: 15960854 | PMCID: PMC1177927
Review Free full text in Europe PMC
Microarray data analysis: from disarray to consolidation and consensus.
Nat Rev Genet, 7(1):55-65, 01 Jan 2006
Cited by: 679 articles | PMID: 16369572
Review
Comparing algorithms for clustering of expression data: how to assess gene clusters.
Methods Mol Biol, 541:479-509, 01 Jan 2009
Cited by: 5 articles | PMID: 19381534
Review