Differences

This shows you the differences between two versions of the page.

--- mkatari-bioinformatics-august-2013-clustering [2014/12/11 14:41] – mkatari
+++ mkatari-bioinformatics-august-2013-clustering [2014/12/11 14:55] – [K-means] mkatari
@@ Line 70: / Line 70: @@
 <code>
-sigGenesMean = rowMeans(sigGenes.normalized)
+# this function takes an vector to be calculated.
-sigGenesSD = apply(sigGenes.normalized, 1, sd)
+scaleData <- function(x) {
+  x = as.numeric(x)
+  meanx = mean(x)
+  sdx = sd(x)
+  y = (x-meanx)/sdx
+  return(y)
+}
+#we need to transpose it because apply function returns the genes as different columns.
+scaledSigGenes = t(apply(sigGenes.normalized, 1, scaleData))
+colnames(scaledSigGenes)=colnames(sigGenes.normalized)
 </code>
 ====== Heatmap ======