[BioC] Memory limitations with AffylmGUI

[James MacDonald]

Malene,

You will probably be better off going to linux, and depending on the
number of chips you will be using in the future, you may even need to
upgrade to a 64 bit chip in order to have sufficient RAM. Attached is a
chart (slightly outdated) showing how much memory is required to read in
various numbers of chips (32 bit windows and linux). An alternate view
of the memory issue can be found here:

http://stat-www.berkeley.edu/users/bolstad/ComputeRMAFAQ/size.html

Best,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> "Malene Herbsleb" <HERBSLEB at KI.AU.DK> 08/09/04 06:52AM >>>
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

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