I have been having problems using gcrma. I have two cases. 1) gcrma on 34 HGU133A chips: in the initial stages memory usage is about 800MB and slowly grows to 1.7GB and then R is hung. 2) Start with 8 HGU133A chips, gcrma processing takes about 45 mins, followed by another 8 HGU133A chips another 45 minutes, then 8 more chips and the memory is up to 1.7GB and R is hung. I am running R 1.8.1 and Bioconductor 1.3 on a 4GB, 2 Xeon Windows box running Windows 2000: gcrma 1.0.0 MASS 7.1-11 reposTools 1.3.5 Biobase 1.4.0 eda 1.8.1 affy 1.3.27 methods 1.8.1 ctest 1.8.1 mva 1.8.1 modreg 1.8.1 nls 1.8.1 ts 1.8.1 base 1.8.1 I also tried R1.9.0-development and Bioconductor development and got the same behavior. I would greatly appreciate any suggestions or pointers or workarounds. Thanks, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html

Hi my impression is that the last dev version of affy, gcrma combined with R1.9dev (12 Jan 2004 version) is more efficient and requires less memory than the previous one. you should update your R version if you have an older one and get the last packages and try again. I m planning to test the same amount of U133A chips very soon with this system using a little less RAM... Hope it helps Philippe