[BioC] justGCRMA memory problem

[Jianping Jin]

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.

regards,

JP-


--On Thursday, February 09, 2006 11:19 AM -0500 Jianping Jin 
<jjin at email.unc.edu> wrote:

> I was reading HG-U133_Plus_2 chips. The total 86 chips I tried to upload.
>
> Thanks!
>
> Jianping
>
> --On Thursday, February 09, 2006 11:06 AM -0500 "James W. MacDonald"
> <jmacdon at med.umich.edu> wrote:
>
>> Jianping Jin wrote:
>>> Hi Jim, thanks for your quick reply!
>>>
>>> I tried --max-mem-size=17000M and run just R 2.2.0 without any other
>>> programs running at the time. The message I got listed as the following:
>>>
>>>> data <- justGCRMA(filenames=files)
>>>
>>> Computing affinities.Computing affinities.Done.
>>> Done.
>>> Adjusting for optical effect..Error: cannot allocate vector of size
>>> 424868 Kb
>>>
>>>> memory.size(max=TRUE)
>>>
>>> [1] 1194139648
>>>
>>>> memory.limit()
>>>
>>> [1] 1782579200
>>>
>>> Any ideas about it?
>>
>> Odd. How many chips and what type are they? Maybe I can try to replicate
>> that here.
>>
>> Jim
>>
>>
>>>
>>> Thanks again!
>>>
>>> Jianping
>>>
>>> --On Thursday, February 09, 2006 10:21 AM -0500 "James W. MacDonald"
>>> <jmacdon at med.umich.edu> wrote:
>>>
>>>> Hi Jianping,
>>>>
>>>> Jianping Jin wrote:
>>>>
>>>>> Dear list:
>>>>>
>>>>> My PC has 2 GB of RAM. I set the max memory size for R equal to 2000M.
>>>>> But  R stopped running when memory size reached 1 GM. Current version
>>>>> I use is  R.2.2.0. I do not run into the problem with R 2.1.0. Does
>>>>> anyone have the  same problem with new version of R?
>>>>
>>>>
>>>> I haven't noticed any differences in memory usage. However, there are
>>>> certain aspects of Windows' memory usage that can cause problems.
>>>> First, if a large block of memory has already been allocated (even if
>>>> it is subsequently freed up), you may not be able to use it. Can you
>>>> replicate the above problem if no other programs are running on your
>>>> computer with a fresh instance of R?
>>>>
>>>> Also, memory.size() will simply give you the amount of RAM that R is
>>>> currently using. More informative would be memory.size(max = TRUE).
>>>>
>>>> Additionally, there is a note in the R-FAQ for Windows that setting the
>>>> memory size > 1.7Gb may be detrimental. I have never seen this problem
>>>> myself, but you might try setting --max.memory.size = 1700M and try
>>>> again.
>>>>
>>>> HTH,
>>>>
>>>> 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
>>>
>>>
>>>
>>>
>>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>>> x Jianping Jin Ph.D.            x
>>> x Bioinformatics scientist      x
>>> x Center for bioinformatics     x
>>> x 3133 Bioinformatics Building  x
>>> x CB# 7104                      x
>>> x University of North Carolina  x
>>> x Chapel Hill, NC 27599         x
>>> x Tel: (919)843-6105            x
>>> x Fax: (919)843-3103            x
>>> x E-mail: jjin at email.unc.edu    x
>>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>>
>>
>> --
>> 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
>
>
>
> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
> x Jianping Jin Ph.D.            x
> x Bioinformatics scientist      x
> x Center for bioinformatics     x
> x 3133 Bioinformatics Building  x
> x CB# 7104                      x
> x University of North Carolina  x
> x Chapel Hill, NC 27599         x
> x Tel: (919)843-6105            x
> x Fax: (919)843-3103            x
> x E-mail: jjin at email.unc.edu    x
> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx



xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
x Jianping Jin Ph.D.            x
x Bioinformatics scientist      x
x Center for bioinformatics     x
x 3133 Bioinformatics Building  x
x CB# 7104                      x
x University of North Carolina  x
x Chapel Hill, NC 27599         x
x Tel: (919)843-6105            x
x Fax: (919)843-3103            x
x E-mail: jjin at email.unc.edu    x
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx