[BioC] Memory limitations with AffylmGUI

[Malene Herbsleb]

Dear list members,
I have a question about memory limitations. I know the issue is frequently debated on the list, and I have checked the archive without finding the answers I need. 
 
I want to use AffylimmaGUI to analyse 80 cel files based on HGU133a chips from Affy. Initially, I tried to analyse the estrogen dataset and it worked very fine. Based on my own data I conducted a target file with the three column headlines Name FileName Target. However, when I open a new file and try to load the cel files throug the target file the loading process starts but then I recieve the message "Not enough memory". I have tried to change the memory allocated to R by the command memory.limit(size=2000). (I started wiht the size=200 and elevated the number.) i also tried to allocate more memory using the target file option under Properties.

I use a 1.6 GHz Intel Pentium M processor, Windows XP and have 1 GB ram. My R version is R 1.9.1.

Now, I consider what solution that will be the best for my future work wiht R, Bioconductor and limma:1)  to upgrade my machine to 2 GB ram - would that be enough to handle my 80 cel files and what number of cel files will be the limit with 2 GB ram?

2) Alternatively, to buy a stationary computer: what would you recommend as a minimum size of processor and memory?

In the long term I will have access to a continuous flow of cel files, so I want a solution that can handle more than "just" my present 80 cel files.

3) Are there any advantages to work on a unix system instead of a windows platform?

I really hope some of you could give me some good advices before I start to convince my superviser that we need to make a big investment.

Thanks in advance!

Best regards,
Malene Herbsleb

 
 
Malene Herbsleb, MSc, Ph.D student
Molecular Diagnostic Laboratory
Aarhus University Hospital, Skejby Sygehus
Brendstrupgaardsvej
DK-8200 Aarhus N
Denmark
+45 89 49 51 29/ +45 89 42 31 31