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
*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
--
Swaraj Basu
PhD Student (Bioinformatics - Functional Genomics)
Animal Physiology and Evolution
Stazione Zoologica Anton Dohrn
Naples
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