On 05/25/2012 06:29 AM, swaraj basu wrote:
Dear All,
I am running R in a system with the following configuration
*Processor: Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
OS: Ubuntu X86_64 10.10
RAM: 24 GB*
The R session info is
*
R version 2.14.1 (2011-12-22)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C *
I have a matrix of dimensions 12 rows X 29318 columns. The matrix contains
numeric as well as NA values. I am using the* rcorr *function from the *
Hmisc* package to get correlation information from the matrix (*
rcorr(matrix)*). During the calculation I get the error "*cannot allocate
vector of size 6.7 GB*". When I check the memory allocation of my R session
I get the following information
Perhaps you are trying to calculate correlations between the 12 rows, so
want to transpose the matrix? If not and if this is a gene expression
study then common practice is to reduce the number of probe sets to
those that are most variable across all samples, as these are the ones
that will provide statistical signal.
Martin
*gc()
used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
Ncells 249638 13.4 467875 25.0 NA 407500 21.8
Vcells 1499217 11.5 2335949 17.9 7000 1970005 15.1
*Can someone please help me in finding a workaround to the problem.
-Regards
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
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