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]]
"Joshi, Nina (NIH/NCI)" <joshini at mail.nih.gov> writes:> 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?Well, it basically means that you're running out of memory. The 523263 KB is just the last request that R tries to honour when it fails, but it is in fact a whole half gigabyte. I forget what the memory usage per Affy chip is (and it depends on the chip, I suppose), but how much did the 10 chips take? Do you have space for 14 times that amount? It is not unlikely that you're running into the limits of the 32bit address space, in which case there is little to do but to move to a 64bit platform (with plenty of swap space). (Note that you may get replies from more specifically experienced people on the Bioconductor lists.) -- O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
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 [[alternative HTML version deleted]] ______________________________________________ R-help at stat.math.ethz.ch 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