I am trying to run justRMA() in R1.8.1 on 110 hgu133plus2 cel files on a Windows 2000 machine with 1 GB RAM, 3.0 GHz processor. I increased the memory allocation with the command memory.limit(1700) It runs for about 10 minutes with the CPU usage almost maxed out, then says "background correcting" at which point, the CPU usage for Rgui.exe comes down to about 4 % and the memmory usage goes up. Soon after that I get a box that says RGui.exe has generated internal errors and will be closed down and the application quits. I would appreciate any help on this. Thanks, Srikanth Jammulapati

The plus2 chips are more than twice the size of the old 133A chips, so I would guess you are running out of memory (I can do ~100 of the 95A chips with 512 Mb of RAM, but I get really close to bombing out). Normally you would get a message saying R was not able to allocate a vector of xxxx bytes, but it might be that you are running out of memory during a call to C code, and that is causing the crash. Ben Bolstad would be more likely to know if that is what is happening. Anyway, RAM is pretty cheap these days so if you are going to be working with that many of the Plus2 chips, you might want to get some more. 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 >>> Srikanth <sjammula@myriad.com> 02/12/04 4:38 PM >>> I am trying to run justRMA() in R1.8.1 on 110 hgu133plus2 cel files on a Windows 2000 machine with 1 GB RAM, 3.0 GHz processor. I increased the memory allocation with the command memory.limit(1700) It runs for about 10 minutes with the CPU usage almost maxed out, then says "background correcting" at which point, the CPU usage for Rgui.exe comes down to about 4 % and the memmory usage goes up. Soon after that I get a box that says RGui.exe has generated internal errors and will be closed down and the application quits. I would appreciate any help on this. Thanks, Srikanth Jammulapati _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor