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

[Steve Lianoglou]

Hi,

On Wed, Nov 3, 2010 at 12:16 PM, Saurin D. Jani <saurin_jani at yahoo.com> wrote:
> Hi BioC,
>
> I am using below function for heatmap.
>
> heatmap.2(FeatureX,col=gmpalette,Colv= FALSE,Rowv = as.dendrogram(hclust(row.dist,method="centroid")),scale="row",key=TRUE,keysize=0.60,symkey=FALSE,density.info="none",trace="none",margins=c(5,5),cexRow=1,cexCol=1,cex.sub=1);
>
>
> Above function, I am getting Genes clustered but not samples

That's because you are setting Colv=FALSE in your call to heatmap.2(...)

> and when I try to cluster samples, I get all control and exp. mixed up.
>
> how can I cluster samples but still be able to keep Controls and Exp. apart in terms of order.
>
> please let me know if anybody performed something like that.

It seems your data is trying to tell you something that you don't want
to hear ...

-- 
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