[BioC] qc

[James W. MacDonald]

Hi Per,

Per.Broberg at astrazeneca.com wrote:
> Dear list
> 
> I tried to run the qc function from simpleaffy on a an object consisting of
> 70 U133A arrays
> 
> However, qc returned an error message indicating problems with allocating
> enough memory. I had set --max-mem-size = 2000Mb.
> 
> What could I do about this?

Windows is problematic in that large chunks of RAM are often not 
available for use even if they have been freed up. You might need to do 
an iterative process. First do all the steps you need to do prior to the 
call to qc(). Then save only those objects you will need for the qc() 
step (using the save() function), then quit R, restart, load() the saved 
objects, and try the qc() step.

If that doesn't work, you just need more RAM. On windows, you can go up 
to 4 Gb, but you will then need to make R 'large address aware'. I 
forget how you do that, but a simple google search or RSiteSearch() 
should come up with something. Unfortunately, you will still only be 
able to use maybe 3 Gb of your RAM, but that may be sufficient.

If that still doesn't work, you could try Linux (you can do a quick 
attempt using Quantian, which boots from CD and has R and BioC 
installed), which is much better at handling memory than windows. If 
that still doesn't work, then you may have to get a 64 bit operating 
system and > 4Gb RAM.

Best,

Jim


> 
>  sessionInfo()
> Version 2.3.1 (2006-06-01) 
> i386-pc-mingw32 
> 
> attached base packages:
> [1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices"
> [7] "utils"     "datasets"  "base"     
> 
> other attached packages:
>  simpleaffy  genefilter    survival     affyPLM       gcrma matchprobes 
>     "2.6.0"    "1.10.1"      "2.26"     "1.8.0"     "2.4.1"     "1.4.0" 
>    affydata        affy      affyio     Biobase     RWinEdt 
>     "1.8.0"    "1.10.0"     "1.0.0"    "1.10.1"     "1.7-4" 
> 
> 
> Cheers
> 
> 
> Per Broberg
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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