[R] memory problem

[James MacDonald]

How many chips you can read is a function of how much RAM you have and
what chip it is. On a unix/linux box you will be able to read in and
process 143 of the HG-u95aV2 chips if you have about 2 Gb RAM. For the
larger U133A chips (RAE/MOE are about the same size), you will probably
need almost twice as much RAM. For the new version 2 chips you will
likely need about four times as much RAM (yep, that's 8 Gb!).

Some information about memory requirements and timings can be found
here:

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

HTH,

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

>>> "Joshi, Nina (NIH/NCI)" <joshini at mail.nih.gov> 03/08/04 12:15PM
>>>
I am trying to upload into R 143 Affymetrix chips onto using R on the
NIH
Nimbus server.  I can load 10 chips without a problem, however, when I
try
to load 143 I receive a error message: cannot create a vector of 523263
KB.
I have expanded the memory of R as follows:  R --min-vsize=10M
--max-vsize=2500M --min-nsize=10M -max-nsize=50M (as specified in help
in
R).  After running this command the memory in R is as follows:  

 

            Used     (Mb)      gc    trigger        (Mb)        limit
(Mb)      

Ncells   513502 13.8        10485760        280.0                1400

Vcells   142525   1.1        162625696     1240.8                2500

 

However, I am still getting the error cannot create a vector of 523263
KB.
Any suggestions/ideas? 

 

Thanks.,

 

Nina

 

Nina Joshi, PhD

NIH/NCI/ Genetics Branch

National Naval Medical Center, Bldg. 8, Rm. 5101

8901 Wisconsin Ave.

Bethesda, MD. 20889-5101

(301) 435-5436 - phone

(301) 496-0047 - fax

 

 


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