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)" <[EMAIL PROTECTED]> 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 [[alternative HTML version deleted]] ______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html ______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html