does change only the colors but dendrograms are unaffected. d <- matrix(rnorm(100),nrow=20) heatmap(d) heatmap(d,scale="column") heatmap(d,scale="row") heatmap(d,scale="none") However scaling clearly affects clustering. see: d <- scale(d) heatmap(d,scale="none") R version 3.0.1 (2013-05-16) -- "Good Sport" Copyright (C) 2013 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) ciao -- Witold Eryk Wolski