I am trying to generate kmean of 10 clusters for a 165 x 165 matrix.
i do not see any errors known to me. But I get this error on running the
script
Error: empty cluster: try a better set of initial centers
the commands are
M <-matrix(scan("R_mutual",n = 165 * 165),165,165,byrow = T)
cl <- kmeans(M,centers=10,20)
len = dim(M)[1]
....
....
I ran the same script last night and it was working prefectly. I have not
made any changes at all !!!And this is very strange. This evening when I ran
the same script i am getting this error. My matrix file is also untouched.
Can any one let me know how to go about this. I must generate 10-mean
clusters
Is there anyother way of doing it ? and how to avoid such error in future?
Asha
http://www.cross-tab.com/surveys/run/test.asp?sid=2026&respid=1 Help us help
you better!
Hi Asha,
kmeans is a non-deterministic routine.
The help page says the following about the centers argument:
centers: Either the number of clusters or a set of initial cluster
centers. If the first, a random set of rows in 'x' are chosen
as the initial centers.
Hence, different choices may lead to different results, ans as you can see
empty clusters. See ?try for a possible workaround if you want to keep using
kmeans.
Best, Ingmar
On 3/31/05 11:08 PM, "Asha Jayanthi" <ashajayanthi at
hotmail.com> wrote:
> I am trying to generate kmean of 10 clusters for a 165 x 165 matrix.
>
> i do not see any errors known to me. But I get this error on running the
> script
>
> Error: empty cluster: try a better set of initial centers
>
> the commands are
>
> M <-matrix(scan("R_mutual",n = 165 * 165),165,165,byrow = T)
>
> cl <- kmeans(M,centers=10,20)
> len = dim(M)[1]
> ....
> ....
>
> I ran the same script last night and it was working prefectly. I have not
> made any changes at all !!!And this is very strange. This evening when I
ran
> the same script i am getting this error. My matrix file is also untouched.
>
> Can any one let me know how to go about this. I must generate 10-mean
> clusters
> Is there anyother way of doing it ? and how to avoid such error in future?
>
> Asha
>
>
> http://www.cross-tab.com/surveys/run/test.asp?sid=2026&respid=1 Help us
help
> you better!
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
--
Ingmar Visser
Department of Psychology, University of Amsterdam
Roetersstraat 15, 1018 WB Amsterdam
The Netherlands
http://users.fmg.uva.nl/ivisser/
tel: +31-20-5256735
Asha Jayanthi wrote:> I am trying to generate kmean of 10 clusters for a 165 x 165 matrix. > > i do not see any errors known to me. But I get this error on running the > script > > Error: empty cluster: try a better set of initial centers > > the commands are > > M <-matrix(scan("R_mutual",n = 165 * 165),165,165,byrow = T) > > cl <- kmeans(M,centers=10,20) > len = dim(M)[1] > .... > .... > > I ran the same script last night and it was working prefectly. I have > not made any changes at all !!!And this is very strange. This evening > when I ran the same script i am getting this error. My matrix file is > also untouched. > > Can any one let me know how to go about this. I must generate 10-mean > clusters > Is there anyother way of doing it ? and how to avoid such error in future?Please read the docs! The help page tells you: "centers: Either the number of clusters or a set of initial cluster centers. If the first, a random set of rows in x are chosen as the initial centers." So, the rows are *randomly* choosen. If this does not work, why don't you specify a fixed set of, e.g., 10 rows? Uwe Ligges> Asha > > > http://www.cross-tab.com/surveys/run/test.asp?sid=2026&respid=1 Help us > help you better! > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html
On Fri, 1 Apr 2005, Asha Jayanthi wrote:> I am trying to generate kmean of 10 clusters for a 165 x 165 matrix. > > i do not see any errors known to me. But I get this error on running the > script > > Error: empty cluster: try a better set of initial centers > > the commands are > > M <-matrix(scan("R_mutual",n = 165 * 165),165,165,byrow = T) > > cl <- kmeans(M,centers=10,20) > len = dim(M)[1] > .... > .... > > I ran the same script last night and it was working prefectly. I have not > made any changes at all !!!And this is very strange. This evening when I ran > the same script i am getting this error. My matrix file is also untouched.It uses a random choice. See the help page, which says so explicitly.> > Can any one let me know how to go about this. I must generate 10-mean > clusters > Is there anyother way of doing it ? and how to avoid such error in future? > > Asha > > > http://www.cross-tab.com/surveys/run/test.asp?sid=2026&respid=1 Help us help > you better! > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html >-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
Asha Jayanthi wrote:> I am trying to generate kmean of 10 clusters for a 165 x 165 matrix. > > i do not see any errors known to me. But I get this error on running the > script > > Error: empty cluster: try a better set of initial centers > > the commands are > > M <-matrix(scan("R_mutual",n = 165 * 165),165,165,byrow = T) > > cl <- kmeans(M,centers=10,20) > len = dim(M)[1] > .... > .... > > I ran the same script last night and it was working prefectly. I have > not made any changes at all !!!And this is very strange. This evening > when I ran the same script i am getting this error. My matrix file is > also untouched. > > Can any one let me know how to go about this. I must generate 10-mean > clusters > Is there anyother way of doing it ? and how to avoid such error in future? > > Asha >Reading ?kmeans we have: centers: Either the number of clusters or a set of initial cluster centers. If the first, a random set of (distinct) rows in 'x' is chosen as the initial centers. So each time you run your analysis kmeans will select 10 random starting values for the cluster centers. Sometimes the selection ends up with no objects in a cluster, sometimes it doesn't - it is random (pseudo) after all. You could provide the centers yourself of course, something along the lines of (adapted from Venables and Ripley (1999) Modern Applied Statistics with Splus, 3rd Edition page 338 - not sure about 4th Ed as my copy is at home just now): M <- data.frame(matrix(rnorm(5000), ncol = 25)) M.x <- as.matrix(M) h <- hclust(dist(M.x), method = "average") initial <- tapply(M.x, list(rep(cutree(h, 10), ncol(M.x)), col(M.x)), mean) M.km <- kmeans(M.x, initial) HTH -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [T] +44 (0)20 7679 5522 ENSIS Research Fellow [F] +44 (0)20 7679 7565 ENSIS Ltd. & ECRC [E] gavin.simpsonATNOSPAMucl.ac.uk UCL Department of Geography [W] http://www.ucl.ac.uk/~ucfagls/cv/ 26 Bedford Way [W] http://www.ucl.ac.uk/~ucfagls/ London. WC1H 0AP. %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%