[BioC] optimizazion cluster in Heatmap

James W. MacDonald jmacdon at med.umich.edu
Thu Nov 8 15:20:45 CET 2007

Hi Alessandro,

I don't think anybody will be able to answer this question for you. If I 
use the same code on the sample.ExpressionSet that comes with the 
Biobase package, it seems to me that the rows are ordered quite well, so 
I wonder what exactly you don't like about the row ordering of your data.

Anyway, there are any number of clustering methods you can use with the 
hclust() function, of which 'average' is only one. You might try some of 
the other clustering methods to see if you get something more to your 



Alessandro Fazio wrote:
> 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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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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