How can I generate SOM clustering from my microarray data and how to see a dendogram view of SOM clustering? -- output of sessionInfo(): > sessionInfo() R version 2.14.0 (2011-10-31) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] class_7.3-3 -- Sent via the guest posting facility at bioconductor.org.

I used this code, taken from http://manuals.bioinformatics.ucr.edu/hom e/R_BioCondManual#R_clustering, the very helpful, for all kinds of things, manuals by T. Gierke at University of California Riverside. library(som) # Loads the required SOM library. y <- matrix(rnorm(50), 10, 5, dimnames=list(paste("g", 1:10, sep=""), paste("t", 1:5, sep=""))) # Creates a sample data set. y <- t(scale(t(y))) # Normalizes the data so that each row has a mean close to zero and a standard deviation of one. y.som <- som(y, xdim = 5, ydim = 6, topol = "hexa", neigh = "gaussian") # Performs SOM clustering. plot(y.som) # Plots SOM clustering result. y.som$visual # Provides the assignment of rows items to the SOM clusters. Remember that the coordinate counting starts here at zero! Juerg ________________________________________ From: bioconductor-bounces@r-project.org [bioconductor- bounces@r-project.org] On Behalf Of Tanay Ghosh [guest] [guest@bioconductor.org] Sent: Tuesday, February 07, 2012 12:08 PM To: bioconductor at r-project.org; tanay.ghosh at inserm.fr Subject: [BioC] SOM clustering How can I generate SOM clustering from my microarray data and how to see a dendogram view of SOM clustering? -- output of sessionInfo(): > sessionInfo() R version 2.14.0 (2011-10-31) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] class_7.3-3 -- Sent via the guest posting facility at bioconductor.org. _______________________________________________ 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