[R] Affymetrix data analysis

[Prof Brian Ripley]

On Fri, 2 Feb 2007, Sicotte, Hugues   Ph.D. wrote:

> Of course, you would know best, so can you tell us if the help pages I
> pull using
>
> help(Memory)
>
> is wrong?
> That help page says (2nd paragraph)
>
> "(On Windows the --max-mem-size option sets the maximum memory
> allocation: it has a minimum allowed value of 16M. This is intended to
> catch attempts to allocate excessive amounts of memory which may cause
> other processes to run out of resources. The default is the smaller of
> the amount of physical RAM in the machine and 1024Mb. See also
> memory.limit.) "

It says nothing about 'half' does it?

Depending on your version of R and Windows, the default is 1Gb, 1.5Gb or 
2.5Gb, and the rw-FAQ gives the whole truth. The current version of that 
help page is different:

https://svn.r-project.org/R/trunk/src/library/base/man/Memory.Rd

it looks like in 2.4.1 it had not been updated yet.

>
>
> Hugues
>
> -----Original Message-----
> From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk]
> Sent: Friday, February 02, 2007 3:05 AM
> To: Sicotte, Hugues Ph.D.
> Cc: Tristan Coram; R-help at stat.math.ethz.ch
> Subject: Re: [R] Affymetrix data analysis
>
> On Thu, 1 Feb 2007, Sicotte, Hugues   Ph.D. wrote:
>
>> Tristan,
>> I have a soft spot for problems analyzing microarrays with R..
>>
>> for the memory issue, there have been previous posts to this list..
>> But here is the answer I gave a few weeks ago.
>> If you need more memory, you have to move to linux or recompile R for
>> windows yourself..
>> .. But you'll still need a computer with more memory.
>> The long term solution, which we are implementing, is to rewrite the
>> normalization code so it doesn't
>> Need to load all those arrays at once.
>>
>> -- cut previous part of message--
>> The defaults in R is to play nice and limit your allocation to half
>> the available RAM. Make sure you have a lot of disk swap space (at
> least
>> 1G with 2G of RAM) and you can set your memory limit to 2G for R.
>
> That just isn't true (R uses as much of the RAM as is reasonable, all
> for
> up to 1.5Gb installed).  Please consult the rw-FAQ for the whole truth.
>
>> See help(memory.size)  and use the memory.limit function
>
> [Please follow the advice you quote.]
>
>> Hugues
>>
>>
>> P.s. Someone let me use their 16Gig of RAM linux
>> And I was able to run R-64 bits with "top" showing 6Gigs of RAM
>> allocated (with suitable --max-mem-size command line parameters at
>> startup for R).
>
> There is no such 'command' for R under Linux.
>
>
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595