Thanks, Sean. Actually I am not expecting I can go too far with this large AffyBatch object even if I make it. But I would like to learn how to create it. Yes, there are a huge number of posts on reading large number of chips and the standalone RMAexpress. Does it do well? Regards, Weiwei On 4/10/07, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > On Tuesday 10 April 2007 16:16, Weiwei Shi wrote: > > Dear Listers: > > > > I read some post about the memory hungry during use of ReadAffy(). I > > > > believe the error I met with was caused by that: > > > Data <- ReadAffy() > > > > Error: cannot allocate vector of size 704969 Kb > > R(397,0xa000d000) malloc: *** vm_allocate(size=721891328) failed (error > > code=3) R(397,0xa000d000) malloc: *** error: can't allocate region > > R(397,0xa000d000) malloc: *** set a breakpoint in szone_error to debug > > R(397,0xa000d000) malloc: *** vm_allocate(size=721891328) failed (error > > code=3) R(397,0xa000d000) malloc: *** error: can't allocate region > > R(397,0xa000d000) malloc: *** set a breakpoint in szone_error to debug > > > > > sessionInfo() > > > > R version 2.4.1 (2006-12-18) > > i386-apple-darwin8.8.1 > > > > locale: > > en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > > > attached base packages: > > [1] "tools" "stats" "graphics" "grDevices" "utils" > > "datasets" "methods" "base" > > > > other attached packages: > > affy affyio Biobase > > "1.12.2" "1.2.0" "1.12.2" > > > > > > My chip sets contains 178 U133A chips and I use 15 out of them for a > > test to create an AffyBatch object and it ends with the size as below: > > Class KB > > Data AffyBatch 55457 > > > > So, I assume I could go around to manually create AffyBatch object by > > "combining" ~12 folds of such sub-objects. But I don't know how. Can > > anyone provide some details about it? > > Hi, Weiwei. > > Look at the help for combine() in the Biobase package. However, remember that > creating such objects, manipulating them, and combining them is likely to > take much more RAM than the individual objects by themselves. > > There are numerous messages in the archives about tricks to get around this > problem using justRMA or some variation or Ben Bolstad's standalone > application. > > Sean > > -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III