Dear all, There are many libraries for the hierarchical clustering in R. However, I can not find one hierarchical clustering by specifically using spearman correlation. Does any experienced guy provide some information? Thank you! Xin LIU This e-mail is from ArraDx Ltd The e-mail and any files transmitted with it are confidential and privileged and intended solely for the use of the individual or entity to whom they are addressed. Any unauthorised direct or indirect dissemination, distribution or copying of this message and any attachments is strictly prohibited. If you have received the e-mail in error please notify helpdesk@arradx.com or telephone +44 28 38 363841 and delete the e-mail from your system. E-mail and other communications sent to this company may be reviewed or read by persons other than the intended recipient. Viruses : although we have taken steps to ensure that this e-mail and any attachments are free from any virus, you should, in keeping with good practice, ensure that they are actually virus free. ArraDx Ltd. Registration Number NI 43067 Registered Address : Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD

Hi If x is my data matrix: c <- cor(x, method="spearman") d <- as.dist(1-c) # because correlation is a similarity measure and you want a distance hc <- hclust(d, method="complete") Mick -----Original Message----- From: Liu, Xin [mailto:Xin.Liu@arradx.com] Sent: 01 November 2004 16:20 To: bioconductor@stat.math.ethz.ch Subject: [BioC] hierarchical clustering - spearman correlation Dear all, There are many libraries for the hierarchical clustering in R. However, I can not find one hierarchical clustering by specifically using spearman correlation. Does any experienced guy provide some information? Thank you! Xin LIU This e-mail is from ArraDx Ltd The e-mail and any files transmitted with it are confidential and privileged and intended solely for the use of the individual or entity to whom they are addressed. Any unauthorised direct or indirect dissemination, distribution or copying of this message and any attachments is strictly prohibited. If you have received the e-mail in error please notify helpdesk@arradx.com or telephone +44 28 38 363841 and delete the e-mail from your system. E-mail and other communications sent to this company may be reviewed or read by persons other than the intended recipient. Viruses : although we have taken steps to ensure that this e-mail and any attachments are free from any virus, you should, in keeping with good practice, ensure that they are actually virus free. ArraDx Ltd. Registration Number NI 43067 Registered Address : Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor

Liu, Xin wrote: > Dear all, > > There are many libraries for the hierarchical clustering in R. > However, I can not find one hierarchical clustering by specifically > spearman correlation. Does any experienced guy provide some information? Hi Xin, you need to keep in mind that these are two separate things: calculation of the distance matrix (i.e. distance between each gene to every other gene), and the actual clustering algorithm to make this matrix into a dendrogram. You can use for example "cor" to calculate correlations including "pearson", "kendall", "spearman", and "hclust" to do the clustering. Best wishes Wolfgang > Thank you! > Xin LIU > > This e-mail is from ArraDx Ltd > > The e-mail and any files transmitted with it are confidential and privileged and intended solely for the use of the individual or entity to whom they are addressed. > > Any unauthorised direct or indirect dissemination, distribution or copying of this message and any attachments is strictly prohibited. > > If you have received the e-mail in error please notify helpdesk@arradx.com or telephone +44 28 38 363841 and delete the e-mail from your system. > > E-mail and other communications sent to this company may be reviewed or read by persons other than the intended recipient. > > Viruses : although we have taken steps to ensure that this e-mail and any attachments are free from any virus, you should, in keeping with good practice, ensure that they are actually virus free. > > ArraDx Ltd. Registration Number NI 43067 > Registered Address : Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD > -- ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Http: www.dkfz.de/abt0840/whuber