I do not want to use the b word, but can anyone who also subscribes to the r-developer list forward my observation regarding heatmap? I am pretty confident that the behaviour of heatmap in R 3.0.1 is not that one intended.
On 31 July 2013 14:03, Witold E Wolski <wewolski at gmail.com> wrote:
Would anyone of the more experienced r-users explain to me the behaviour of the scale parameter in the heatmap function. different options for scale (R 3.0.1) do change only the colors but do not affect the dendrograms. Please see for yourself executing the following code: d <- matrix(rnorm(100),nrow=20) stats::heatmap(d) X11() heatmap(d,scale="column") X11() heatmap(d,scale="row") X11() heatmap(d,scale="none") In all four above cases the dendrograms look exactly the same However, scaling clearly affects clustering. see: d <- scale(d) heatmap(d,scale="none") best regards R version 3.0.1 (2013-05-16) -- "Good Sport" ciao -- Witold Eryk Wolski -- Witold Eryk Wolski
Witold Eryk Wolski