[BioC] bicluster

[Weiwei Shi]

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
>
> --
> Ramón Díaz-Uriarte
> Bioinformatics
> Centro Nacional de Investigaciones Oncológicas (CNIO)
> (Spanish National Cancer Center)
> Melchor Fernández 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