[BioC] justGCRMA memory problem

[Jianping Jin]

Thanks for your time, Jim! I will try that.
best,
JP-

--On Thursday, February 09, 2006 4:14 PM -0500 "James W. MacDonald" 
<jmacdon at med.umich.edu> wrote:

> Jianping Jin wrote:
>> Hi Jim,
>> FYI I ran justRMA on R 2.1.0 and it was fine:
>>
>>
>>> files <- dir(pattern="CEL")
>>> data<- justRMA(filenames=files)
>>
>> Background correcting
>> Normalizing
>> Calculating Expression
>>
>>> memory.size(max=TRUE)
>>
>> [1] 1536868352
>>
>>> memory.limit()
>>
>> [1] 1572864000
>>
>> I ran into the same problem when I ran justGCRMA on R 2.1.0 as on R
>> 2.2.0.
>
> Yeah, I am a little thick today it seems. Your error message was 'cannot
> allocate vector of size 424868 Kb' and your memory.size(max = TRUE) ==
> 1194139648
>
> You add those up (noting that the vector is listed in *Kb*), and you get
> 1618007648 bytes, which is probably less RAM than you have available for
> R (Windows XP takes quite a bit of RAM for itself).
>
> You could always get more RAM, but you will have to make R 'large address
> aware' to be able to access more than 2 Gb (IIRC). I believe this means
> you have to build R from source as well. There is something in the R-FAQ
> for Windows about this issue.
>
> Best,
>
> Jim
>
>
>
>>
>> regards,
>>
>> JP-
>>
>
> --
> 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



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