Question

Access the probe ids associated with each cluster

0

Entering edit mode

Wendy Qiao ▴ 360

@wendy-qiao-4501

Last seen 9.6 years ago

Hi all, I am doing a hierarchical clustering for 12,000 genes across 3 samples. The gene expression is stored in a matrix called 'Gexpr' which is a 12000 by 3 matrix. I plot the cluster using heatmap.2(Gexpr, Rowv=TRUE, Colv=FALSE,dendrogram="row",col=greenred(75),trace="none",dendrogram ="column") I was finding a way to access the probe id's for one of the clusters. Could anybody please give me some suggestions? Thank you very much, Wendy [[alternative HTML version deleted]]

Clustering probe Clustering probe • 1.0k views

ADD COMMENT • link updated 13.1 years ago by Steve Lianoglou ★ 13k • written 13.1 years ago by Wendy Qiao ▴ 360

score 0 · Answer 1 · 2011-03-27

0

Entering edit mode

Steve Lianoglou ★ 13k

@steve-lianoglou-2771

Last seen 13 months ago

United States

Hi Wendy, On Sun, Mar 27, 2011 at 7:43 PM, Wendy Qiao <wendy2.qiao at="" gmail.com=""> wrote: > Hi all, > > I am doing a hierarchical clustering for 12,000 genes across 3 samples. The > gene expression is stored in a matrix called 'Gexpr' which is a 12000 by 3 > matrix. > > I plot the cluster using > > heatmap.2(Gexpr, Rowv=TRUE, > Colv=FALSE,dendrogram="row",col=greenred(75),trace="none",dendrogram > ="column") > > I was finding a way to access the probe id's for one of the clusters. Could > anybody please give me some suggestions? The `heatmap.2` function "invisibly" returns a list/structure with lots of stuff in it. Look in the "Value" section in the ?heatmap.2 help documentation -- I guess you're most interested in the `rowInd` and `rowDendrogram` stuff. Look through the documentation for ?dendrogram (and the stuff in the "See Also" sections), too. -steve -- 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

ADD COMMENT • link 13.1 years ago Steve Lianoglou ★ 13k

0

Entering edit mode

Thanks a lot, Steve. This is really helpful. Wendy On 27 March 2011 20:30, Steve Lianoglou <mailinglist.honeypot@gmail.com>wrote: > Hi Wendy, > > On Sun, Mar 27, 2011 at 7:43 PM, Wendy Qiao <wendy2.qiao@gmail.com> wrote: > > Hi all, > > > > I am doing a hierarchical clustering for 12,000 genes across 3 samples. > The > > gene expression is stored in a matrix called 'Gexpr' which is a 12000 by > 3 > > matrix. > > > > I plot the cluster using > > > > heatmap.2(Gexpr, Rowv=TRUE, > > Colv=FALSE,dendrogram="row",col=greenred(75),trace="none",dendrogram > > ="column") > > > > I was finding a way to access the probe id's for one of the clusters. > Could > > anybody please give me some suggestions? > > The `heatmap.2` function "invisibly" returns a list/structure with > lots of stuff in it. > > Look in the "Value" section in the ?heatmap.2 help documentation -- I > guess you're most interested in the `rowInd` and `rowDendrogram` > stuff. Look through the documentation for ?dendrogram (and the stuff > in the "See Also" sections), too. > > -steve > > -- > 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 > [[alternative HTML version deleted]]

ADD REPLY • link 13.1 years ago Wendy Qiao ▴ 360