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