Re: [R] hclust() memory issue

2011-03-14 Thread Thomas Lumley
> From: "Ochsner, Scott A" > > > Sent: Mon, March 14, 2011 2:19:57 PM > Subject: RE: [R] hclust() memory issue > > John, > > First, why are you trying to cluster so many rows?  Presumably, if this is a > gene expression array dataset, most of the array featu

Re: [R] hclust() memory issue

2011-03-14 Thread array chip
, TX 77030 Voice: (713) 798-6227 Fax: (713) 790-1275 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of array chip Sent: Monday, March 14, 2011 4:03 PM To: r-help@r-project.org Subject: [R] hclust() memory issue Hi, I have a microarray

Re: [R] hclust() memory issue

2011-03-14 Thread Ochsner, Scott A
) 798-6227 Fax: (713) 790-1275 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of array chip Sent: Monday, March 14, 2011 4:03 PM To: r-help@r-project.org Subject: [R] hclust() memory issue Hi, I have a microarray dataset of dimension

[R] hclust() memory issue

2011-03-14 Thread array chip
Hi, I have a microarray dataset of dimension 25000x30 and try to clustering using hclust(). But the clustering on the rows failed due to the size: > y<-hclust(dist(data),method='average') Error: cannot allocate vector of size 1.9 Gb I tried to increase the memory using memory.limit(size=3000), s