error in kmeans
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
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