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--- mkatari-bioinformatics-august-2013-clustering [2014/12/15 12:46] – mkatari
+++ mkatari-bioinformatics-august-2013-clustering [2014/12/15 12:48] – mkatari
@@ Line 108: / Line 108: @@
   for (i in 2:20) {
      kmeans_tmp=kmeans(x, i, nstart=25)
-     kmeans_ss[i] = kmeans_tmp$betweenss/kmeans_tmp$totss
+     #alternate way of looking at proportion of ss that is provided by between groups.
+     #kmeans_ss[i] = kmeans_tmp$betweenss/kmeans_tmp$totss
+     #using silhouette width to evaluate clusters.
+     kmeans_sil= (kmeans_tmp$betweenss-kmeans_tmp$withinss)/max(kmeans_tmp$betweenss, kmeans_tmp$withinss)
+     kmeans_ss[i] = mean(kmeans_sil)
   }
   return(kmeans_ss)