[BioC] steps to manually build AffyBatch object

[Weiwei Shi]

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.

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