Hi:
   
     I'm clustering a microarray dataset with a large # of samples.  I would like your opinion on the best way to automatically determine the optimal # of clusters.  Currently I am using the "cluster" package, clustering with "clara", examining the average silhouette width at various numbers of clusters.  I'd like opinions on whether any newer packages offer better determination of optimal # of clusters, considering the algorithms in "cluster" were developed decades ago.  By the way, I have alot of missing values in my dataset, coded as "NA", so some software packages don't work.
   
     Here is the code I've been using:
   
  library(cluster)
  avgsil <- c()
  
for (k in  kseq){
  clarares <- clara(data, k, rngR = TRUE)
  savg <- clarares$silinfo$avg.width
  print(c(k,savg))
  avgsil[k] <- savg
}
  k<-kseq
plot(k,avgsil[k])
lines(k,avgsil[k])
   
  Sincerely,
   
  Andrew McSweeny
  grad student
  Medical University of Ohio

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