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

[Sean Davis]

---------- 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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