[BioC] bicluster

[Thomas Girke]

I guess rows and columns are mixed up in this example. Here is how it
should work for non-square matrices:

x <- matrix(rnorm(500,10,2),100,50)
hr <- as.dendrogram(hclust(as.dist(cor(t(x),method="pearson"))))
hc <- as.dendrogram(hclust(as.dist(cor(x, method="spearman"))))
hv <- heatmap(x, Rowv=hr, Colv=hc)
	
Thomas

	
On Thu 09/21/06 14:39, Weiwei Shi wrote:
> hi again:
> 
> I modified some codes from
> http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.html#R_clustering
> 
> to do a simple biclustering. On both dimensions, I used pearson
> distance. When x is a square matrix, it works; while x is not a square
> matrix, there is an error. So I am wondering if there is a way to do
> the job for the latter since on microarray analysis, the matrix is not
> a square for most of time. Please correct me if
> 1. i should not use the same pearson distance on both direction
> 2. any other problems causing the error.
> 
> > x <- matrix(rnorm(1000,10,2),100,100); hc <- as.dendrogram(hclust(as.dist(cor(t(x), method="pearson")))); hr <- as.dendrogram(hclust(as.dist(cor(x, method="pearson")))); hv <- heatmap(x, Rowv=hr, Colv=hc)
> 
> > x <- matrix(rnorm(1000,10,2),100,200); hc <- as.dendrogram(hclust(as.dist(cor(t(x), method="pearson")))); hr <- as.dendrogram(hclust(as.dist(cor(x, method="pearson")))); hv <- heatmap(x, Rowv=hr, Colv=hc)
> Error in heatmap(x, Rowv = hr, Colv = hc) :
>         row dendrogram ordering gave index of wrong length
> 
> 
> On 9/21/06, Ramon Diaz-Uriarte <rdiaz at cnio.es> wrote:
> > On Wednesday 20 September 2006 23:29, Weiwei Shi wrote:
> > > Dear listers:
> > >
> > > I searched the literature and failed to find some public tools used
> > > for biclustering analysis in microarray application. I am wondering if
> > > there is one in bioconductor or somewhere else?
> >
> > Dear Weiwei,
> >
> > I don't think there are BioC tools for this. But there is R/S code for at
> > least:
> >
> > - the Plaid model, in a set of functions from Heather Turner (don't have the
> > URL here, but you'll find it googling); this is a reimplementation of the
> > Lazzeroni & Owen approach, with some differences.
> >
> > - the COSA approach of Friedman & Meulman (google for "COSA Friedman")
> >
> >
> > Best,
> >
> > R.
> >
> >
> > >
> > > thanks
> >
> > --
> > Ram?n D?az-Uriarte
> > Bioinformatics
> > Centro Nacional de Investigaciones Oncol?gicas (CNIO)
> > (Spanish National Cancer Center)
> > Melchor Fern?ndez Almagro, 3
> > 28029 Madrid (Spain)
> > Fax: +-34-91-224-6972
> > Phone: +-34-91-224-6900
> >
> > http://ligarto.org/rdiaz
> > PGP KeyID: 0xE89B3462
> > (http://ligarto.org/rdiaz/0xE89B3462.asc)
> >
> >
> >
> > **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
> > **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
> >
> >
> 
> 
> -- 
> Weiwei Shi, Ph.D
> Research Scientist
> GeneGO, Inc.
> 
> "Did you always know?"
> "No, I did not. But I believed..."
> ---Matrix III
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 

-- 
Thomas Girke, Ph.D.
1008 Noel T. Keen Hall
Center for Plant Cell Biology (CEPCEB)
University of California
Riverside, CA 92521