[BioC] clustering of genes

Laurent Gautier laurent at cbs.dtu.dk
Fri May 16 07:24:47 MEST 2003


Hi,

The packages 'mva', 'cluster' and 'cclust' are sure places to shop
if you want to do clustering with R.
>From my experience, many will listen to you as you elaborate about
clustering, but will conlude with "it is like Eisen's clustering ?"
(those red and green plot probably contain subliminal messages ;) ). 
To do "kinda the same" when this is an absolute requisite,
I use something like:

dist.likeEisen <- function(x, use="all.obs") {
  c.x <- cor(x, use=use)
  a.x <- acos(c.x)
  return(as.dist(a.x)) 
}

hc <- hclust(dist.likeEisen(exprs(eset)))



Hopin' it helps,



L.

-- 
- 
--------------------------------------------------------------
currently at the National Yang-Ming University in Taipei, Taiwan
--------------------------------------------------------------
Laurent Gautier			CBS, Building 208, DTU
PhD. Student			DK-2800 Lyngby,Denmark	
tel: +45 45 25 24 89		http://www.cbs.dtu.dk/laurent

On Fri, May 16, 2003 at 01:01:21PM +1000, Gordon Smyth wrote:
> I would like advice about software and appropriate approaches for 
> clustering genes.
> 
> I have results from a series of 45 cDNA arrays comparing RNA sample 
> extracted from a hela human cell line. My collaborators have over-expressed 
> a dozen different transcription factor proteins and compared the results 
> back to a reference. There are 3-4 replicate arrays for each transcription 
> factor. I have classified each gene as likely up, down, neither for each 
> transcription factor. Now I would like to do a cluster analysis of the 
> genes. I know that there is a long tradition of cluster algorithms for 
> microarray results in the cancer context, but I don't have any experience 
> with clustering using R.
> 
> What software have people found useful for this problem? There are the 
> cluster and class packages on CRAN, both of which look promising. Is there 
> anything on bioconductor or anything in R specifically directed at 
> microarray results?
> 
> Many thanks
> Gordon
> ---------------------------------------------------------------------------------------
> Dr Gordon K Smyth, Senior Research Scientist, Bioinformatics,
> Walter and Eliza Hall Institute of Medical Research,
> 1G Royal Parade, Parkville, Vic 3050, Australia
> Tel: (03) 9345 2326, Fax (03) 9347 0852,
> Email: smyth at wehi.edu.au, www: http://www.statsci.org
> 
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