steps to manually build AffyBatch object
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Weiwei Shi ★ 1.2k
@weiwei-shi-1407
Last seen 9.6 years ago
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? Thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III
GO affy affyio GO affy affyio • 924 views
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@sean-davis-490
Last seen 12 weeks ago
United States
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
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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
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