[BioC] Affymetrix data analysis

[James W. MacDonald]

Hi Tristan,

Tristan Coram wrote:
> Hi,
> 
>  
> 
> I am trying to read in my Affymetrix CEL files (48 files, total ~600 MB) but
> I keep getting memory errors.  Can somebody please help me with this.  Or is
> therea remote server I can send my data to for computation?

You don't say anything about your OS, version of R, sessionInfo(), 
amount of RAM, etc, etc, so really there is very little anybody can say 
for sure (this is like calling a mechanic on the phone and saying 'My 
car won't run. Can you help me?').

Some general prescriptives:

1.) Get more RAM. It's cheap these days.
2.) Use justRMA() or justGCRMA().
3.) Use a 64-bit OS with lots of RAM.
4.) If on windows or linux, you can use RMAexpress (google to find).

HTH,

Jim


> 
>  
> 
> Any help is much appreciated.
> 
>  
> 
> Thanks
> 
>  
> 
>  
> 
> Dr. Tristan Coram
> 
> Postdoctoral Research Associate
> 
> Research Plant Pathologist/Geneticist
> 
>  
> 
> United States Department of Agriculture
> 
> Agricultural Research Service
> 
> Wheat Genetics, Quality Physiology & Disease Research
> 
>  
> 
> 209 Johnson Hall
> 
> Washington State University
> 
> Pullman, WA 99163
> 
>  
> 
> Office: +1 509 335-1596  Fax: +1 509 335-2553
> 
> Email: tcoram at mail.wsu.edu
> 
>  
> 
>  
> 
> 
> 	[[alternative HTML version deleted]]
> 
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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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