[BioC] creating platformdesign affy_250k nsp

[James W. MacDonald]

Roel Verhaak wrote:
> Dear List,
> 
> In order to use the oligo library for analysis of Affymetrix snparrays, 
> I have tried to create a PlatformDesign using the makePlatformDesign 
> package. I have been doing this on a 64-bit Linux machine, with 4Gb RAM, 
> using R2.4a and BioC 1.9. After three days of running, I have stopped 
> the process; memory use had increased to 5Gb so it was swapping and 
> disturbing other processes. It has been displaying 'Creating 
> environment...' since it started.
> 
> My question is: does this process really takes this long or did it 
> crash, and do I have more chance on success when I run this with more 
> memory?

It probably didn't crash. It takes me ~2-3 hours to build using 64-bit 
Linux and 8 gb RAM, so I think you just need more RAM. Once you start 
swapping, things really slow down.

Best,

Jim


> 
> Thanks,
> Roel
> 
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-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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