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

[Saurin D. Jani]

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. 

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...

so, ctrl1 and ctrl 5 are next to each other and Exp1 and Exp5 are next to each other. 

Thanks,
Saurin



--- On Wed, 11/3/10, Steve Lianoglou <mailinglist.honeypot at gmail.com> wrote:

> From: Steve Lianoglou <mailinglist.honeypot at gmail.com>
> Subject: Re: [BioC] heatmap Clustering help, two class (Control vs Exp) Experiments,
> To: saurin_jani at yahoo.com
> Cc: "Bioconductor Bioconductor" <bioconductor at stat.math.ethz.ch>
> Date: Wednesday, November 3, 2010, 12:34 PM
> 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
>