[BioC] How to search for coexpression?

[David Ruau]

If you already have a subset of chosen probesets you want to look at, 
you can perform a hierarchical clustering on it to see the probesets 
that are co-expressed in the same condition (it can tell you some infos 
if your list is not too big). Just one approach among many others...
Take a look at the heatmap function from the simpleaffy package.

 > library(simpleaffy)
 > library(amap)
 > e.eset <- exprs(eset)
 > heatmap(e.eset, col= blue.white.red.cols, 
distfun=function(c){Dist(c,method="pearson")}, labCol=colnames(e.eset), 
Rowv=cov(e.eset), hclustfun=function(c){hclust(c,method='mcquitty')})

David

N.B: have also a look at: http://www.bepress.com/bioconductor/

On Mar 7, 2006, at 12:09, stueber at mpiz-koeln.mpg.de wrote:

> Dear colleaques,
>
> After reading data from affymetrix CEL files I would like to
> get information about coexpressed and non-coexpressed genes for
> a chosed set of probesets.
>
> I start with:
>
>> library(affy)
>> Data <- ReadAffy()
>> eset <- rma(Data)
>
> This give me a big array of all intensities for
> all probesets and experiments.
> But what to do then?
>
> Any hints appreciated.
>
> Kurt Stueber
>
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