[BioC] increase memory size in R, problem reading 67 affy CEL files

[James MacDonald]

R is not complaining that it cannot allocate a total of 700Mb, but that
it ran out of memory at a point where it was trying to allocate 700Mb to
a certain task.

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
>>> "Dipl.-Ing. Johannes Rainer" <johannes.rainer at tugraz.at> 11/26/04
1:57 AM >>>
thanks a lot!

but when i have 2GB physical memory and 6GB of virual one, how is it
possible
that R runs out of memory because it can not allocate a vector of 700MB?
but
anyway, i will use the justRMA and everything is fine.

thanks again


Quoting James MacDonald <jmacdon at med.umich.edu>:

> If I am not mistaken, R simply takes whatever memory is available
under
> linux (unlike win32 where you have the --max-memory-size flag), so if
> you are running out of memory all you can do is get more.
>
> And yes, justRMA() does exactly the same as ReadAffy() followed by
> rma(), only without an AffyBatch that can be used for certain QC
plots,
> etc.
>
> Best,
>
> Jim
>
>
>
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>>>> "Dipl.-Ing. Johannes Rainer" <johannes.rainer at tugraz.at> 11/25/04
> 11:47 AM >>>
> hi,
>
> i want to read in 67 CEL files (hgu133plus2 chips), but i get
everytime
> the
> error message: "Error: cannot allocate vector of size 709203KB"
> i run R (version 2.0.1, bioconductor 1.5) on a linux workstation with
2
> GB
> physical RAM and 6 GB swap space... so there should not be any problem
> regarding the memory installed on the system. is there a possibility
to
> increase the memory that can be allocated by R?
> other question: the justRMA() function, does this function exactly the
> same as
> ReadAffy() and then rma() ?
>
> thanks for your help!
>
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