Hi all, I would like to validate my clustering based on Pearson correlation coefficients. I found that somebody have adapted clusterStab from Euclidean distance matrix to Pearson correlation coefficient matrix. I was wondering if the adapted code is publicly available. Do you have any other suggestions for validating the number of clusters from Pearson correlation coefficients? Thank you in advance, Wendy [[alternative HTML version deleted]]

Hi Wendy, On 4/16/2011 6:12 PM, Wendy Qiao wrote: > Hi all, > > I would like to validate my clustering based on Pearson correlation > coefficients. I found that somebody have adapted clusterStab from Euclidean > distance matrix to Pearson correlation coefficient matrix. I was wondering > if the adapted code is publicly available. Do you have any other suggestions > for validating the number of clusters from Pearson correlation coefficients? Due to popular request (like three times in the last five years ;-D), I have added a 'distmeth' argument to both clusterComp() and benhur(). Valid choices are "euclidean" (default) and "pearson". If you choose "pearson", then the distance measure will be 1-cor(<yourdatahere>). This is in the devel branch, version 1.25.1 and will be propagated through the build system in the next couple of days. You don't technically need the devel version of R to use it, just download the correct version for your OS and install. Best, Jim > > Thank you in advance, > Wendy > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues