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]] > > > > ______________________________________________ > > [EMAIL PROTECTED] 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 > > > > > > ______________________________________________ > [EMAIL PROTECTED] 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 > ______________________________________________ [EMAIL PROTECTED] 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
