[BioC] steps to manually build AffyBatch object

[Sean Davis]

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