
Hello everybody, I have a problem in doing a cluster with Heatmap. Briefly, I want a cluster with fixed column order and row order depending on the dendrogram produced by the clustering method. BUT, it seems that the row sorting is not optimal, that is genes with similar expression profiles are not group tpgrther but spread. This is the code I used: > mydist <- function(x) cor.dist(x)> myhclust <- function(x) hclust(x, method='average')> heatmap(exprs(exampleSet),Colv=NA, dist=mydist, hclust=myhclust) > sessionInfo()R version 2.5.0 (2007-04-23) i386-pc-mingw32 locale:LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252attached base packages:[1] 'splines'   'tools'     'stats'     'graphics'  'grDevices' 'utils'    [7] 'datasets'  'methods'   'base'     other attached packages:    bioDist          GO  genefilter    survival         ALL   Rgraphviz geneplotter     '1.8.0'    '1.16.0'    '1.14.1'      '2.31'     '1.4.3'    '1.14.1'    '1.14.0'     lattice    annotate     Biobase        RBGL       graph    '0.15-4'    '1.14.1'    '1.14.0'    '1.12.0'    '1.14.2' ANY idea about what I should do to have a good row sorting? THANK you in advance Regards, Alessandro
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