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

[Saurin D. Jani]

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?

Thank you so much,
Saurin 



--- On Tue, 11/2/10, Sean Davis <sdavis2 at mail.nih.gov> wrote:

> From: Sean Davis <sdavis2 at mail.nih.gov>
> Subject: [BioC] Fwd:  how to plot corr between two tissues/dendrograms
> To: abosco at email.arizona.edu
> Cc: "Bioconductor Newsgroup" <bioconductor at stat.math.ethz.ch>
> Date: Tuesday, November 2, 2010, 9:38 PM
> ---------- 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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