# [BioC] bicluster

Thomas Girke thomas.girke at ucr.edu
Sat Sep 23 06:38:12 CEST 2006

```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)
> >
> >
> >
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> >
> >
>
>
> --
> Weiwei Shi, Ph.D
> Research Scientist
> GeneGO, Inc.
>
> "Did you always know?"
> "No, I did not. But I believed..."
> ---Matrix III
>
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--
Thomas Girke, Ph.D.
1008 Noel T. Keen Hall
Center for Plant Cell Biology (CEPCEB)
University of California
Riverside, CA 92521

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