[BioC] Fwd: how to plot corr between two tissues/dendrograms

[Saurin D. Jani]

Hi Thomas,

you are correct...thats right...last image is like Sean sent me in PDF...fantastic. I will explore more ape resource..

thank you so much,
Saurin

--- On Wed, 11/3/10, Thomas Girke <thomas.girke at ucr.edu> wrote:

> From: Thomas Girke <thomas.girke at ucr.edu>
> Subject: Re: [BioC] Fwd:  how to plot corr between two tissues/dendrograms
> To: "Sean Davis" <sdavis2 at mail.nih.gov>
> Cc: abosco at email.arizona.edu, "Bioconductor Newsgroup" <bioconductor at stat.math.ethz.ch>
> Date: Wednesday, November 3, 2010, 1:35 PM
> The phylogenetics package ape on CRAN
> has a variety of tree plottings facilities 
> that come close to what you are looking for:
> http://cran.at.r-project.org/web/packages/ape/index.html
> 
> For instance, take a look at the last image on their
> screenshot site: 
> http://ape.mpl.ird.fr/ape_screenshots.html
> 
> In general, ape is a very nice resource for customizing
> trees for gene
> expression, phylogenic or many other use cases.
> 
> Thomas
> 
> 
> On Tue, Nov 02, 2010 at 09:38:25PM -0400, Sean Davis
> wrote:
> > ---------- Forwarded message ----------
> > From: abosco at email.arizona.edu
> <abosco at 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 at 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 at mail.nih.gov>:
> > 
> > > On Mon, Nov 1, 2010 at 7:35 PM, <abosco at 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
> 
> 
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