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?
Best regards,
Anthony Bosco
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
[[alternative HTML version deleted]]
It sounds like he wants to align the dendrograms and plot the R^2 for
expression at each concordant split. False?
OP: This sounds an awful lot like biclustering, why not just look
into
that?
On Tue, Nov 2, 2010 at 6:08 PM, Sean Davis <sdavis2@mail.nih.gov>
wrote:
> 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
>
> [[alternative HTML version deleted]]
>
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--
If people do not believe that mathematics is simple, it is only
because they
do not realize how complicated life is.
John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html="">
[[alternative HTML version deleted]]
