[BioC] heatmap Clustering help, two class (Control vs Exp) Experiments,

[Steve Lianoglou]

Hi Saurin,

On Wed, Nov 3, 2010 at 12:43 PM, Saurin D. Jani <saurin_jani at yahoo.com> wrote:
> Hi,
>
> You are right but When I do this:
>
> heatmap.2(FeatureX,col=gmpalette,Colv=as.dendrogram(hclust(col.dist,method="average")), Rowv=as.dendrogram(hclust(row.dist,method="average")),scale="row",key=TRUE,keysize=0.60,symkey=FALSE,density.info="none",trace="none",margins=c(5,MapMargin),cexRow=1,cexCol=1,cex.sub=1);
>
> my control and exp. samples get mixed up..!! is there anyway I can pass a parameter ..not to do that just cluster samples on control and then exp. so, sorted view will be there.

But why would you cluster the samples to begin with, if you just want
to reorder them in some (your) arbitrary way?

Assuming your data is properly nomralised, etc. and clustering your
samples "mixes them up," then the heatmap is showing you visually that
your treatment examples aren't "strikingly different" than your
controls. Your data is trying to tell you that (apparently) all of
these experiments kind of look (expression wise) like each other.

Maybe that's telling you something about the quality of your data, or
its annotation?

Maybe you can try the plotPCA function in the affycoretools package as
another way to see how your experiments "cluster together".

I'm not sure that it would change things, but what happens if you
remove all probes w/ low variance across your entire dataset and
re-cluster them?

> May be something like this: cluster control samples then exp. samples and then cluster based on Signal Intensity. so, I keep the order ctrl1,ctrl5,ctrl6,ctrl2,... and then Exp1,Exp5,Ex2,Exp10 ....so on...

But then this is kind of misrepresenting what one would expect to see
in such a plot .. you could, of course, plot and save heatmaps over
just your control data, then again with just your experiment, then
photoshop them together, but ... what's the point?

I guess the question is: what are you trying to show in the heatmap
you are trying to  produce?

Given that, people might be able to then suggest things you could try.

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact