You might try posting to R-devel to get a response. Looking at the source for heatmap, it does seem to be a "feature" rather than a bug since the cluster analysis is performed well before any scaling is applied. Would heatmap(scale(X)) accomplish what you want?
------------------------------------- David L Carlson Associate Professor of Anthropology Texas A&M University College Station, TX 77840-4352 -----Original Message----- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Witold E Wolski Sent: Monday, August 5, 2013 3:17 AM To: r-help@r-project.org Subject: [R] When scale is applied in heatmap When clustering I would do something like plot(hclust(dist(scale(X)))) In case of heatmap and heatmap.2 it seems to me that for the dendrograms plot(hclust(dist(X))) is done while for the heatmap image(scale(X)) is done. I would say this is a bug however, because this is consistent among the heatmap functions, can anyone enlighten me why this is so? -- Witold Eryk Wolski ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.