[BioC] Heatmap.2 scale problems: Sacling inside the function gives different results than scaling outside!!!

[Elmer Fernández]

Dear Users
I'm working with the heatmap.2 function and I realize that if you use the
scale input paramenter gives different results than usign the scale function
outsie and feed the heatmap.2 fucntion with the scaled matrix. I attached
the results of the two approaches and the used data matrix (M.csv).
SO, what I'm doing wrong?

R Code

library(gplots)
M=matrix(c(rnorm(10*3,1,2),rnorm(10*2,-0.5,1)),ncol=5)
heatmap.2(M,scale="column",trace="none",main="scaled inside")
x11();heatmap.2(scale(M),scale="none",trace="none",main="scaled outside")

> sessionInfo()
R version 2.10.0 (2009-10-26)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8          LC_NUMERIC=C
LC_TIME=en_US.UTF-8           LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8       LC_MESSAGES=en_US.UTF-8
LC_PAPER=en_US.UTF-8          LC_NAME=en_US.UTF-8
 [9] LC_ADDRESS=en_US.UTF-8        LC_TELEPHONE=en_US.UTF-8
LC_MEASUREMENT=en_US.UTF-8    LC_IDENTIFICATION=en_US.UTF-8

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods
base

other attached packages:
[1] gplots_2.7.4   caTools_1.10   bitops_1.0-4.1 gdata_2.7.1
gtools_2.6.1   rkward_0.5.1

loaded via a namespace (and not attached):
[1] tools_2.10.0


-- 
Elmer A. Fernández (Bioing. PhD)
Investigador Asistente CONICET - Research Assistant CONICET
Prof. Inteligencia Artificial -UCC - Prof. Artificial Intelligence @ UCC
tel: +54-(0)351-4938000 int 145
Fax: +54-(0)351-4938081
web page : http://www.uccor.edu.ar/modelo.php?param=3.8.5.15
http://sites.google.com/site/biologicaldatamininggroup/Home/
mail address: Camino Alta Gracia Km 7.1/2- Córdoba-5017-Argentina