[BioC] R memory limit

[Kasper Daniel Hansen]

If you're on a mac and you only have 4GB of memory you will likely not
get very much additional memory by going 64bit, as the 32bit version
is capable of using 3GB and you also need ram for the OS.  It is very
likely that you will not be ale to run your analysis on your machine.

There are 3 possibilities.  (1) See if you can get by using justRMA,
(2) move to a machine with more RAM, (3) use a package that is
designed to run in limited memory like aroma.affymetrix of xps.

If you don't have access to a machine with more memory, you should
investigate (3).

Kasper

On Mon, Jun 14, 2010 at 10:01 AM, Benilton Carvalho
<beniltoncarvalho at gmail.com> wrote:
> FYI: the latest R is 2.11.1, so my recommendation is to upgrade.
>
> If you installed R.app (ie, you have R under /Applications) you should
> have R64.app there too...
>
> If you're using the terminal, load R using
>
> R --arch x86_64
>
> You will need to reinstall the packages in order to use them in 64 bit.
>
> b
>
> On 14 June 2010 14:57, Hernando Martínez <hernybiotec at gmail.com> wrote:
>> sorry, I am trying to analize an expression microarray of nearly 350
>> samples. My R version is R 2.10.1 GUI 1.31 Leopard build 32-bit (5537). How
>> do I load R in 64 bit? (maybe this is a trivial question for you but it is
>> not for me, as I have no computer background).
>> Thank you very much again,
>> Hernando
>>
>> 2010/6/14 Benilton Carvalho <beniltoncarvalho at gmail.com>
>>>
>>> You didn't provide us the information described in the post guide
>>> (sessionInfo and description of the issue).
>>>
>>> R does not impose any limit.
>>>
>>> What is the type of array you're trying to analyze? And what
>>> preprocessing strategy would you like to apply? How many samples do
>>> you have? Are you using R in 32 or 64 bit mode?
>>>
>>> You may be interested in taking a look at justRMA(), if RMA is your
>>> choice. If you're in 32 bit mode, you definitely want to load R in 64
>>> bit...
>>>
>>> With more detailed information, we're going to be able to help you out.
>>>
>>> b
>>>
>>> On 14 June 2010 14:36, Hernando Martínez <hernybiotec at gmail.com> wrote:
>>> > Hi, I am working with large data, and when I try to read it into R using
>>> > 'ReadAffy', I get the following error message: "cannot allocate a vector
>>> > size 712Mb". I have a MacBook Pro with 4Gb of memory. I have been
>>> > reading
>>> > some posts online, but I haven't found a clear solution. Maybe is a
>>> > limit in
>>> > R, or an imposed limit of my system that I should change. Does anyone
>>> > knows
>>> > how to do it? Any ideas?
>>> >
>>> > Many thanks,
>>> >
>>> > --
>>> > Hernando Martínez Vergara
>>> >
>>> >        [[alternative HTML version deleted]]
>>> >
>>> >
>>> > _______________________________________________
>>> > Bioconductor mailing list
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>>> >
>>
>>
>>
>> --
>> Hernando Martínez Vergara
>>
>
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