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
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