Hi all, I've read here that nobody had a problem running gcRMA on Linux. Surprisingly I do. I run 36 HG-U133_Plus_2 cel files using 1G of RAM and 2G of swapping memory and get this message Error: cannot allocate vector of size 359894 Kb Note that regular RMA runs just fine. Then I read specifications for gcRMA and found recommendation to have 1.25G of RAM. So I've upgraded my machine to 1.5G and got exactly the same message Error: cannot allocate vector of size 359894 Kb. What else could you recommend to solve the problem? Is it feasible to split gcRMA runs then combine data in Excel and normalize it using column average? Thank you Dmitry

Dmitry wrote: > Hi all, > > I've read here that nobody had a problem running gcRMA on Linux. > Surprisingly I do. > I run 36 HG-U133_Plus_2 cel files using 1G of RAM and 2G of swapping memory > and get this message > Error: cannot allocate vector of size 359894 Kb > Note that regular RMA runs just fine. > > Then I read specifications for gcRMA and found recommendation to have 1.25G > of RAM. > So I've upgraded my machine to 1.5G and got exactly the same message > Error: cannot allocate vector of size 359894 Kb. > > What else could you recommend to solve the problem? justGCRMA() is designed to solve this problem. HTH, Jim > Is it feasible to split gcRMA runs then combine data in Excel and normalize > it using column average? > > Thank you > > Dmitry > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- 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