RE: [R] hclust error

From: Adaikalavan Ramasamy <ramasamy_at_cancer.org.uk>
Date: Tue 20 Jul 2004 - 01:56:07 EST

Herman,

Just out of curiosity, have you tried Mike Eisen's software Cluster (http://rana.lbl.gov/EisenSoftware.htm). Try version 2.12 instead as version 2.20 appears to give wrong results.

I never tried with 32000 rows, but when I tried a 10000 row last year it seem to produce the results in a few minutes whereas R took either too long or ran out of memory. Let us know if it works.

I assume you are trying to cluster the rows/genes here in which case the number of columns/samples will not matter in your case.

Regards, Adai.

On Mon, 2004-07-19 at 16:14, Liaw, Andy wrote:
> This has been asked on R-help several times in the past.
>
> The `dist' object for the data of that size would be:
>
> > 32513*32512/2
> [1] 528531328
>
> To store a vector of that size in double precision (8 bytes), you'd need:
>
> > 32513*32512/2*8/1024^2
> [1] 4032.374
>
> I.e., that's nearly 4 GB. Is your computer capable of doing that?
>
> Andy
>
> > From: Herman, David (NIH/NIMH)
> >
> > Hello,
> > I'm trying to do a cluster analysis on a large
> > data set. I
> > tried it out with a smaller one first, but I got this error:
> >
> > > hc<-hclust(dist(x),"ave")
> > Error: cannot allocate vector of size 4129151 Kb
> >
> > The data sample used (i.e. "x") is a numerical data set of
> > size 32513 by 31
> >
> > Does anyone know how I can do this analysis? Is R capable of
> > this data
> > size?
> > Ultimately I wanna do an analysis on a dataset of size 32513 by 220
> >
> >
> > Thanks!
> >
> > dave
> >
> >
> >
> > [[alternative HTML version deleted]]
> >
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R-help@stat.math.ethz.ch mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Tue Jul 20 02:05:53 2004

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