[R] subsetting the gene list

[Adaikalavan Ramasamy]

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.
>