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

Steve Lianoglou mailinglist.honeypot at gmail.com
Wed Nov 3 17:34:02 CET 2010


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

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