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. Fern?ndez (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- C?rdoba-5017-Argentina