R help - Sep 2008 - subsetting the gene list

Hi all,

I am working on a single color expression data using limma. I would like to
perform a cluster analysis after selecting the differentially genes based on
the P value (say 0.001). As far as my knowledge is concerned I have to do
the sub setting of these selected genes on the normalized data (MA), to
retrieve the distribution across the samples.
But I am wondering whether I can perform using the R script?
I would appreciate any help.

-- 

Regards,
Abhilash

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Have you tried reading some of the material from the BioConductor 
workshop http://bioconductor.org/workshops/ ?

Here is a simplistic way of proceeding:

  ## Calculate pvalues from t-test
  p <- apply( mat, function(x) t.test( x ~ cl )$p.value )

  ## Subset
  mat.sub <- mat[ p, ]

  ## Cluster
  heatmap(m)

Regards, Adai




Abhilash Venu wrote:
> Hi all,
> 
> I am working on a single color expression data using limma. I would like to
> perform a cluster analysis after selecting the differentially genes based
on
> the P value (say 0.001). As far as my knowledge is concerned I have to do
> the sub setting of these selected genes on the normalized data (MA), to
> retrieve the distribution across the samples.
> But I am wondering whether I can perform using the R script?
> I would appreciate any help.
>