search for: som

...a good picture. There is probably a much easier solution since R is changing and becoming more convenient to use. I i'm also including the code of the example i'm doing f.std.data<-function(x) { return((x-mean(x,na.rm=T))/sd(x,na.rm=T)) } # Read data, and standardize before running SOM d.music<-read.csv("music-sub.csv",row.names=1) d.music.std<-cbind(d.music[,c(1,2)],apply(d.music[,-c(1,2)],2,f.std.data)) # Load libraries library(rggobi) library(som) # Run SOM music.som<-som(d.music.std[,-c(1:2)],6,6,neigh="bubble",rlen=100) music.som<-som(d....

...a good picture. There is probably a much easier solution since R is changing and becoming more convenient to use. I i'm also including the code of the example i'm doing f.std.data<-function(x) { return((x-mean(x,na.rm=T))/sd(x,na.rm=T)) } # Read data, and standardize before running SOM d.music<-read.csv("music-sub.csv",row.names=1) d.music.std<-cbind(d.music[,c(1,2)],apply(d.music[,-c(1,2)],2,f.std.data)) # Load libraries library(rggobi) library(som) # Run SOM music.som<-som(d.music.std[,-c(1:2)],6,6,neigh="bubble",rlen=100) music.som<-som(d....

R version 2.9.2 (2009-08-24) - for windows > library(SOM) Error in library(SOM) : there is no package called 'SOM' Where can I get the SOM library from? Thanks in advance -- View this message in context: http://old.nabble.com/SOM-library---where-do-I-find-it-tp26415633p26415633.html Sent from the R help mailing list archive at Nabble.com.

Bug in "SOM" package in R. This simple code withot for loop runs:-------simple.r-------- library(som) A <- as.matrix(read.table("C:/code/h.txt", sep="\t", header=TRUE, row.names=1)) print(som(A,1,2)$visual) print(som(A,1,3)$visual) ---------------------------------------- The...

All, The kohonen predict function is returning NA for SOM predictions regardless of data used... even the package example for a SOM using wine data is returning NA's Does anyone have a working example SOM. Also, what is the purpose of trainY, what would be the dependent data for an unsupervised SOM? As may be apparent to you by my questions, I am very...

I am trying to use SOM package to cluster some gene expression data. I got stuck with 2 questions and can't not find any documents to resolve these matters. I would really appreciate if anybody can shed some sort of light. Q1. I clustered the data using SOM function and plotted it using plot function. But I can't...

Hi all, I originally posted this to the bioconductor group, but maybe it's better suited to the r-help... I'm using som() to partition samples of gene expression data into clusters. The point is to classify control vs. experimental cases (sample clustering). The original matrix was 22283 x 8. The 8 samples have 4 controls and 4 experimentals. I transposed the matrix so that its dim are 8 x 22283, and called that...

Hi. Three years ago, I've read the question of availability of SOM library for R using Kohonen's SOM_PAK in this mailing-list. This answer was no availability. And no package dealing with SOM in CRAN. Is this situation same? Could you tell me availability this library? Best Regards.

I am trying to understand how the SOM algorithm works using library(class) SOM function. I have a 1000*10 matrix and I want to be able to summarize the different types of 10-element vectors. In my real world case it is likely that most of the 1000 values are of one kind the rest of other (this is an oversimplification). Say for example...

...bles, and about 8000 instances (or objects/rows/samples). In addition I have one more ('class') variable that I have about 10 instances for, but for which I wish to impute values for. I am a little confused how to go about doing this, mostly as I'm not well-versed in it. Do I train the SOM with a data object that contains just the first 10 variables (exclude the 'class' variable), then predict using an object that has all of the variables (including the class variable)? (I am using the kohonen package, and in general I am using the SOM technique as a comparison to some other...

Hi all, I have a question about the SOM routine. You can either supply the initial representatives for the lattice yourself or else they are chosen randomly from the dataset. Is it possible to pass the random-seed as an argument somehow, when choosing the random initialisation of the lattice? As it is now, each time I run a SOM on a...

Is there an implementation of the SOM ('Self Organizing Map') procedure in R ? I am aware of the implementations of Sammon mapping, multidimensional scaling and, somewhat peripherally, principal curves and projection pursuit .. but not SOM per se as far as I can see. Am I missing something? --------------------- for a...

...let me introduce myself: my name is Jonck van der Kogel and I am a graduate student at the Erasmus University of Rotterdam. I am currently working on my thesis which is on the use of artificial intelligence for large data-sets. To do an analysis of a certain data-set I want to use Kohonen's SOM algorithm. However, as I understand it, the SOM algorithm as it's implemented in R only gives a visual representation of the topological mapping. I want to do further analysis with this mapping and thus I need to do a clustering of the topological mapping produced by the SOM. I was wonderin...

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Hi All, I'm looking for some reference paper about SOM (self organizing map) algorithm. I tried the paper which is mentioned in the help page of function "som (package:som)": http://www.cis.hut.fi/research/papers/som_tr96.ps.Z But I can't open it for some reason. Could you please help me with it ? T...

somfunc<- function (file) { aa_som<-scale(file) final.som<-som(data=aa_som, rlen=10000, grid=somgrid(5,4, "hexagonal")) pdf(file="/home/cdu/changbin/file.pdf") #output graphic file. plot(final.som, main="Unsupervised SOM") dev.off() } I have many different...

Hi All, I am still learning R, but making, IMO, great strides. I learned about Kohonen/Self-Organizing Maps in class and I would like to try to replicate some of the things we have seen in class. Below is my code. I am trying to create a u-matrix. In the documentation on page 9 it appears the type of plot, dist.neighbours should do the trick, however, I am getting an error: (Error in match.arg(type) : 'arg' should be one of "codes",...

...server is Fedora 5, OpenLdap version 2.3.19-4. I've got it so smbd and nmbd start properly and I can use a windows box and see the domain using srvmgr.exe and usrmgr.exe. I'm then able to signon from a windows XP computer with the command net use \\pdcserver\ipc$ /user:root rootpassword Some things that aren't working right... please excuse the long post but I thought I'd try to include some relevant files before being asked, to save some trouble. 1) some of the groups defined in ldap do not show up in usrmgr.exe. net groupmap list produces Domain Admins (S-1-5-21-2256156...

...GUI front-end has encountered a problem and needs to close. We are sorry for the inconvenience." it happens also that the window disppeared without message error Please, if you have already see this problem or if you understand it and know the solution, please contact me... code: results.som <- matrix(NA, 7, 7) results.sil <- matrix(NA, 7, 7) results.dbi <- matrix(NA, 7, 7) results.dun <- matrix(NA, 7, 7) for (i in 8:14){ for (j in 8:14){ # SOM with Kohonen package som <- som(data.scaled, grid = somgrid(i, j, "hexagonal"), radius=j, rlen=1000) # Summ...

Dear list, I read the SOM package manual but I don't understand how to perform (for example) 1) the SOM analysis on Iris data 2) with a visualization similar to that of figure 7 in http://www.cis.hut.fi/projects/somtoolbox/package/papers/techrep.pdf Any suggestion? Thanks in advance, Gianandrea -- View this message in...