Hi, Once I have loaded an x by y gene expression matrix (x genes by y time points), how do I get a matrix of gene-gene correlation? I'm looking for a speedy method rather than the method with the latest greatest clustering algorithm... although the latter would be great ;-) Thanks for any help, Dan. -- Chat to R users in your area now! irc://irc.freenode.net/#R [[alternative HTML version deleted]]

You can use the cor() function like this: ## Some example data set y <- matrix(rnorm(50), 10, 5, dimnames=list(paste("g", 1:10, sep=""), paste("t", 1:5, sep=""))) ## Create correlation matrix c <- cor(t(y), method="spearman"); ## Convert to distances d <- as.dist(1-c) On Thu, May 07, 2009 at 05:27:21PM +0100, Dan Bolser wrote: > Hi, > > Once I have loaded an x by y gene expression matrix (x genes by y time > points), how do I get a matrix of gene-gene correlation? > > I'm looking for a speedy method rather than the method with the latest > greatest clustering algorithm... although the latter would be great ;-) > > > Thanks for any help, > Dan. > > > -- > Chat to R users in your area now! > irc://irc.freenode.net/#R > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 >