Dear All,
I am using Silhouette to estimate the number of clusters in a microarray
dataset.
Initially, I used the iris data to test my piece of code as follows:
library(cluster)
data(iris)
mydata<-iris[,1:4]
maxk<-15 # at most 15 clusters
myindex<-rep(0,maxk) # hold the si values for each k clusters
mdist<-1-cor(t(mydata)) #dissimlarity
mdist<-as.dist(mdist)
for(k in 2:maxk)
{
hc<-diana(mdist,diss =TRUE, stand = FALSE)
si<-silhouette.default(cutree(as.hclust(hc),k=k),mdist)
myindex<-summary(si)$avg.width
}
myk<-rev(order(myindex))[1] #select the number of k clusters with the
#largest si value
I met the following problems:
> for(k in 2:maxk)
+ {
+ hc<-diana(mdist,diss =TRUE, stand = FALSE)
+ si<-silhouette.default(cutree(as.hclust(hc),k=k),mdist)
+ myindex<-summary(si)$avg.width
+ }
Error in "[<-"(*tmp*, iC, "sil_width", value = s.i) :
number of items to replace is not a multiple of replacement length
In addition: Warning messages:
1: longer object length
is not a multiple of shorter object length in: b.i - a.i
2: number of rows of result
is not a multiple of vector length (arg 2) in: cbind(mmm, as.vector(each))
Could any one help me how I can solve the problems???
Your kind help is highly appreciated!!
ping
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