[BioC] som - can it divide the samples into clusters

[Sean Davis]

You can use kmeans clustering which takes a number of clusters as a 
parameter.  Also, you can use hierarchical clustering (see ?hclust) and 
cutree (see ?cutree) to cluster samples and then divide them into 
classes based on the clustering.

Sean

On Aug 12, 2004, at 8:20 AM, Liu, Xin wrote:

> Hi,
>
> Such as in Golub data, he divide the data into four groups by setting 
> the group number as 4 in SOM. IF I use condition tree or principal 
> component analysis, I can not set the group number by myself.
>
> Xin
>
> -----Original Message-----
> From: Sachin Mathur [mailto:smathur at kumc.edu]
> Sent: 11 August 2004 16:46
> To: Liu, Xin
> Subject: Re: [BioC] som - can it divide the samples into clusters
>
>
>
> Hi,
>
> You can cluster the samples in GS by using the condition tree and find
> out the relations from the branch length or use principal component
> analysis.
>
> Sahin.
>
>>>> "Liu, Xin" <Xin.Liu at arragen.com> 8/11/2004 3:22:05 AM >>>
> Dear all,
>
> Somebody used a SOM to divide the samples into clusters. However the
> SOM in GeneSpring only divides the genes into clusters, not samples. I
> wonder the SOM in R can divide the samples? Or anybody knows a SOM can
> do this work? Thanks a lot!
>
> Xin LIU
>
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