[BioC] affy & problems with memory

[Ben Bolstad]

David,

RMAExpress can process an essentially unlimited number of arrays of any
chip type. You can download the latest version at
http://RMAExpress.bmbolstad.com

As output it produces a tab delimited text file. You should have little
difficulty importing this into R.

Best Wishes,

Ben

On Thu, 2006-01-12 at 14:40 +0100, kfbargad at ehu.es wrote:
> Hi, 
> 
> would it be a solution to use RMAexpress to obtain expression values 
> for a good amount of arrays and then import them into your R session? 
> I haven´t got much experience on this program but it is said on the 
> RMAexpress webpage that the program can process upto 250 arrays 
> simultaneously ( I guess not U133plus) and in the history section it 
> is stated that the 0.4alpha3 version can run 200 arrays. 
> 
> Any information on U133plus?
> 
> David
> 
> > My apologies for the previous (empty) mail, it slipped me :)
> > 
> > > I'm currently working on that chip type myself on a system with 
> 512MB RAM
> > > and had to increase the memory assigned to R too. However
> > > "--max-mem-size=1024Mb" seems to be ok in my case. Besides the 
> problem of
> > > how much memory is necessary for the hgu133plus2 maybe somebody 
> out there
> > > could answer me this two related questions:
> > > * I'm running R under WinXp AND under Linux on the same machine. 
> However
> > > there has never been any memory problem in linux. So is the memory
> > > allocation or the  assignment of the max. memory size that can be 
> used by R
> > > different in the two systems?
> > 
> > This is due to the much more flexible memory management of Linux as 
> > opposed to Windows. Theoretical limit on a 32-bit Windows machine as 
> > 2Gb; 4 Gb under Linux. Linux has also a more flexible way of 
> swapping 
> > (finding memory on your local harddrive) then Windows (the /swp 
> > filesystem).
> > 
> > 
> > > * With my 512MB RAM system the old maximum memory value under 
> WinXP was
> > > 512MB. Is this just a coincidence or does this maximum value rise 
> to 1024MB
> > > if I upgrade my system to 1024MB RAM?
> > 
> > No, this is not a coincidence since the maximum value is related to 
> the 
> > amount available on your system.
> > 
> > Cheers,
> > R.
> > 
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> > Bioconductor at stat.math.ethz.ch
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> >
> 
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