Ask on the bioconductpr mailing list, where you will be diirected to
several solutions for analyzing what I guess are 100's is cel files
http://bioconductor.org
--
Martin Morgan
On Dec 11, 2009, at 8:02 AM, Marc Schwartz <marc_schwa...@me.com> wrote:
On Dec 11, 2009, at 6:24 AM, Ambrosi Alessandro wrote:
Dear all, I am meeting some problems with memory allocation. I
know it is an old issue, I'm sorry.
I looked for a solution in the FAQs and manuals, mails, but without
finding the working answer.
I really hope you can help me.
For instance, if I try to read micorarray data I get:
mab=ReadAffy(cdfname="hgu133plus2cdf")
Error: cannot allocate vector of size 858.0 Mb
I get similar errors with smaller objects, smaller data sets or
other procedures
("Error: cannot allocate vector of size 123.0 Mb").
I'm running R with Suse 11.1 Linux OS, on two Xeon processors (8
cores), 32 GB RAM.
I suppose I have enough resources to manage these objects and data
files....
Any suggestions or hints will be really appreciated!
Many thanks in advance.
Alessandro
Well, you are running into a situation where there is not a
contiguous chunk of RAM available in the sizes referenced, for
allocation to the vector.
Presuming that you are running a 64 bit version of SUSE (what does
'uname -a' show in a system console), you should also check to be
sure that you are also running a 64 bit version of R. What does:
.Machine$sizeof.pointer
show?
If it returns 4, then you are running a 32 bit version of R, which
cannot take advantage of your 64 bit platform. You should install a
64 bit version of R.
HTH,
Marc Schwartz
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