Problems with clValid: "fanny unable to find clusters"
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Jörg ▴ 40
@jorg-3228
Last seen 9.9 years ago
Hello, I have been working a lot with the clValid package lately. I find it a really helpful, well written and documented package. However, I ran into a problem and hope someone can help me: Using this command: " clust=clValid(obj=matrix,nClust=2:8,validation=c("internal", "stability"),metric ="euclidean", method ="average",neighbSize = 10,maxitems =dim(matrix)[1], clMethods = c("fanny"))" I receive the following messages: Warning messages: 1: In vClusters(mat, clMethods[i], nClust, validation = validation, : fanny unable to find 4 clusters, returning NA for these validation measures 2: In vClusters(mat, clMethods[i], nClust, validation = validation, : fanny unable to find 5 clusters, returning NA for these validation measures ...(repeats until 8 clusters) There are no fuzzy clusters computed for k=4..8 However, using fanny directly there is no warning message at all (the same for k=4..8): fanny(x=matrix,k=5,metric ="euclidean",maxit = 500) Note that maxit=500 is the standard and not reached for any of the clusters. Interestingly using metric ="correlation" reports no warnings for clValid. Any idea what the problem might be? Thanks a lot J?rg --
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@herve-pages-1542
Last seen 57 minutes ago
Seattle, WA, United States
Hi J?rg, Even if it suggests a few BioC packages, clValid is not a BioC package (it's hosted on CRAN). You will get better results if you ask directly to its authors/maintainer (see DESCRIPTION file). Cheers, H. J?rg Linde wrote: > Hello, > > I have been working a lot with the clValid package lately. I find it a really helpful, well written and documented package. However, I ran into a problem and hope someone can help me: > > Using this command: > " > clust=clValid(obj=matrix,nClust=2:8,validation=c("internal", "stability"),metric ="euclidean", method ="average",neighbSize = 10,maxitems =dim(matrix)[1], clMethods = c("fanny"))" > > I receive the following messages: > > Warning messages: > 1: In vClusters(mat, clMethods[i], nClust, validation = validation, : > fanny unable to find 4 clusters, returning NA for these validation measures > 2: In vClusters(mat, clMethods[i], nClust, validation = validation, : > fanny unable to find 5 clusters, returning NA for these validation measures > > ...(repeats until 8 clusters) > There are no fuzzy clusters computed for k=4..8 > However, using fanny directly there is no warning message at all (the same for k=4..8): > fanny(x=matrix,k=5,metric ="euclidean",maxit = 500) > > Note that maxit=500 is the standard and not reached for any of the clusters. > Interestingly using metric ="correlation" reports no warnings for clValid. > > Any idea what the problem might be? > > Thanks a lot > J?rg > > -- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
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