On Mon, May 3, 2010 at 8:39 AM, varpal singh <gilvarpal@gmail.com> wrote:

> Respected Sir,
>
> I'm varpal singh, I'm writting to express my interest in clustering.
> According your suggestio I got some good results with bioconductor. Now I
> have got 847 genes after  criteria (P value 0.05 and fold change -1><1  )
> within wild type and mutant each have two replicate.
>
> I have some problem like:
>
> Can we do Clustering on the basis of expression value always ?
> how can we decide which coefficent is perfect (coef =1 or ceof=2) ?
> Plz find out attachment in which some screen shot of my results... (in
> which up - down - and both genes clustered separetly..)
> But I cant see clearly name of genes on the cluster, plz tell me how can
> see ??
>

For visualizing 847 gene names, you should consider using a cluster viewer
like java treeview.  You can use the ctc package to export in a format that
treeview understands.

And R-only alternative is to make the plots as large pdf files using the
pdf() device and specifying a very large height.

Sean

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