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--- mkatari-bioinformatics-august-2013-clustering [2014/12/11 14:55] – [K-means] mkatari
+++ mkatari-bioinformatics-august-2013-clustering [2014/12/11 15:11] – [K-means] mkatari
@@ Line 82: / Line 82: @@
 scaledSigGenes = t(apply(sigGenes.normalized, 1, scaleData))
 colnames(scaledSigGenes)=colnames(sigGenes.normalized)
+#now to run k-means
+SigGenes.kmeans.2 = kmeans(scaledSigGenes, 2)
+# a measure of how well the clustering has performed
+# it is the sum of squares between members of the outside group and sum of squares total
+# higher the better.
+SigGenes.kmeans.2$betweenss/SigGenes.kmeans.2$totss
+#to get the genes in the different clusters
+SigGenes.kmeans.2.group1 = names(which(SigGenes.kmeans.2$cluster==1))
+SigGenes.kmeans.2.group2 = names(which(SigGenes.kmeans.2$cluster==2))
 </code>