On Wed, Nov 3, 2010 at 2:26 PM, Saurin D. Jani <saurin_jani@yahoo.com>wrote:

> Hi Sean,
>
> thanks for your email and PDF ..that looks fantastic..The Image with
> Heatmap...of two tissues...That exactly I am looking for..!!
>
> In my case..two tissues..I have one Normalized set of TWO classes Control
> and Experimental..will that work?
>
> Do you have R code for that or should I ask author for this?
>
>
There is no R code.  This thread began by a user asking for a way to create
that PDF.  Thomas Girke just replied that there might be a similar
functionality in the ape package.

Sean



> Thank you so much,
> Saurin
>
>
>
> --- On Tue, 11/2/10, Sean Davis <sdavis2@mail.nih.gov> wrote:
>
> > From: Sean Davis <sdavis2@mail.nih.gov>
> > Subject: [BioC] Fwd:  how to plot corr between two tissues/dendrograms
> > To: abosco@email.arizona.edu
> > Cc: "Bioconductor Newsgroup" <bioconductor@stat.math.ethz.ch>
> > Date: Tuesday, November 2, 2010, 9:38 PM
> > ---------- Forwarded message
> > ----------
> > From: abosco@email.arizona.edu
> > <abosco@email.arizona.edu>
> > Date: Tue, Nov 2, 2010 at 9:28 PM
> > Subject: Re: [BioC] how to plot corr between two
> > tissues/dendrograms
> > To: "Davis, Sean (NIH/NCI) [E]" <sdavis2@mail.nih.gov>
> >
> >
> > Hi Sean,
> >
> >
> > Thanks for your email.
> >
> > I have attached the figure in PDF..
> >
> > To clarify, each cluster dendrogram represents the gene
> > coexpression pattern
> > within each tissue, and the blue links represent gene-gene
> > correlations
> > between
> > tissues (ie similar idea to Dobrin et al. Genome Biol.
> > 2009;10(5):R55.
> > Epub 2009
> > May 22).
> >
> > The idea is to construct gene coexpression modules for each
> > tissue
> > independently, then quantify molecular interactions between
> > the two tissues.
> >
> >
> > Best regards,
> >
> >
> > Anthony Bosco
> >
> >
> >
> > Quoting Sean Davis <sdavis2@mail.nih.gov>:
> >
> > > On Mon, Nov 1, 2010 at 7:35 PM, <abosco@email.arizona.edu>
> > wrote:
> > >
> > >> Dear list,
> > >>
> > >>
> > >> I have some microarray data in which gene
> > expression was profiled in two
> > >> different tissues, collected at the same time from
> > the same subjects.
> > >>
> > >> I would like to use hierarchical clustering
> > initially to cluster the gene
> > >> expression patterns separately for each tissue.
> > >>
> > >> Then I would like to correlate gene expression
> > traits between the two
> > >> tissues,
> > >> and plot the two cluster dendrograms together with
> > links representing the
> > >> between tissue correlations of the clustered genes
> > in a single plot (see
> > >> hypothetical example in the attached powerpoint
> > slide).
> > >>
> > >> The problem is that I do not know how to go about
> > plotting this in R.
> > >>
> > >> Can anyone please point me in the right
> > direction?
> > >>
> > >>
> > > Hi, Anthony.  Powerpoint get's scrubbed, I
> > think.  You may have to put up
> > a
> > > link to the slide.  I have to admit, I'm not
> > clear on what you want to do.
> > >
> > > Sean
> >
> > -----Inline Attachment Follows-----
> >
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>
>
>

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