[BioC] heatmap Clustering help, two class (Control vs Exp) Experiments,
Saurin D. Jani
saurin_jani at yahoo.com
Wed Nov 3 17:43:23 CET 2010
You are right but When I do this:
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.
--- 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
> On Wed, Nov 3, 2010 at 12:16 PM, Saurin D. Jani <saurin_jani at yahoo.com>
> > Hi BioC,
> > I am using below function for heatmap.
> > heatmap.2(FeatureX,col=gmpalette,Colv= FALSE,Rowv =
> > Above function, I am getting Genes clustered but not
> That's because you are setting Colv=FALSE in your call to
> > 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
> 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
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