my major is bioinformatics, and i'm trying to cluster ( agglomerate the closest pari of observations ) in R. i have already got my own similarities metric, but do not know how to clust it based on similarities instead of dissimilarities. since the help document of hierclust mentions the parameter "sim", which seems good to me, but it doesn't appear in the code of hierclust() function again? and no sample about it. so could anybody please help me as author? thanks in advance xinan yang xinan at molgen.mpg.de
Hi! I would convert the simmilarities into dissimilarities by myself. Its quite easy. For example to make a dissimilarity from correlation which is a simmilarity measures you can: dcorr = 1 - cor and dcorr will be a dissimilarity. More general. Make the smallest value the largest and the largest the smallest. And ensure that the transformation is monotonical. Sincerely Eryk *********** REPLY SEPARATOR *********** On 6/10/2004 at 9:06 AM Xinan Yang wrote:>>>my major is bioinformatics, and i'm trying to cluster ( agglomerate >>>the closest pari of observations ) in R. >>> >>> >>>i have already got my own similarities metric, but do not know how to >>>clust it based on similarities instead of dissimilarities. >>> >>> >>>since the help document of hierclust mentions the parameter "sim", >>>which seems good to me, but it doesn't appear in the code of >>>hierclust() function again? and no sample about it. so could anybody >>>please help me as author? >>> >>>thanks in advance >>> >>>xinan yang >>>xinan at molgen.mpg.de >>> >>>______________________________________________ >>>R-help at stat.math.ethz.ch mailing list >>>https://www.stat.math.ethz.ch/mailman/listinfo/r-help >>>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.htmlDipl. bio-chem. Eryk Witold Wolski @ MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel: 0049-30-83875219 / \ mail: wolski at molgen.mpg.de ---W-W---- http://www.molgen.mpg.de/~wolski
As I've already said on the R-devel list,
MM> why on earth are you using hierclust() from the ORPHANED package
MM> 'multiv', when there's hclust() in the core
'stats' package
MM> and 'agnes' in the recommended 'cluster' package ?
{and your question is not about hierclust but about dissimilarities and has
already been answered}.
Regards,
Martin Maechler