Scott, thanks for the suggestion. I have already filtered genes from more than 30000. Probably I should filter more. I will take a look at genefilter package.
John ________________________________ From: "Ochsner, Scott A" <sochs...@bcm.edu> <r-help@r-project.org> 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 features are not going to change across treatments/conditions and will be relatively uninformative. Try using a filter which does not use treatment/condition information to decrease the number or array features you are attempting to cluster. There are numerous examples in the affycoretools and genefilter packages from Bioconductor http://www.bioconductor.org/. HTH, Scott Scott A. Ochsner, PhD One Baylor Plaza BCM130, Houston, 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 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), still got the same error. I also tried agnes() from cluster package and pvclust() from pvclust package without success. My computer has 2G memory. Is there a more memory efficient clustering packages available? Thanks John > sessionInfo() R version 2.11.1 (2010-05-31) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pvclust_1.2-1 cluster_1.13.1 rat2302cdf_2.6.0 simpleaffy_2.24.0 gcrma_2.20.0 genefilter_1.30.0 affy_1.26.1 [8] Biobase_2.8.0 loaded via a namespace (and not attached): [1] affyio_1.16.0 annotate_1.26.1 AnnotationDbi_1.10.2 Biostrings_2.16.9 DBI_0.2-5 IRanges_1.6.16 [7] preprocessCore_1.10.0 RSQLite_0.9-2 splines_2.11.1 survival_2.35-8 tools_2.11.1 xtable_1.5-6 [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
