I am trying to use RMA for soybean chips. I have a problem with RMA causing segmentation fault. I get Background correcting Normalizing Calculating Expression Segmentation Fault It does not happen for the small chips like yeast or mouse. I wonder if it is related with memory allocation when the C functions get called since soybean chip has more than 60,000 genes. Any suggestions are welcome. Thanks, Hua Li

On Thu, Nov 04, 2004 at 08:30:42AM -0500, Hua Li wrote: > > I am trying to use RMA for soybean chips. I have a problem with RMA causing > > segmentation fault. I get > Background correcting > Normalizing > Calculating Expression > Segmentation Fault > > It does not happen for the small chips like yeast or mouse. I wonder if it > is related with memory allocation when the C functions get called since > soybean chip has more than 60,000 genes. > > Any suggestions are welcome. You might try (if on Unix) running R in a debugger, R -d ddd or R -d gdb and seeing if you can help us to track down the problem - as it stands it is pretty hard to say. It could be size (but I doubt it), it could be that someone is accessing in the wrong spot; I am not sure that last time that affy was run through something like valgrind to check for leaks or inappropriate accessing. Robert > > Thanks, > > Hua Li > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+

Hua Li wrote: > > I am trying to use RMA for soybean chips. I have a problem with RMA causing > > segmentation fault. I get > Background correcting > Normalizing > Calculating Expression > Segmentation Fault > > It does not happen for the small chips like yeast or mouse. I wonder if > it is related with memory allocation when the C functions get called > since soybean chip has more than 60,000 genes. > > Any suggestions are welcome. In the immediate: The use 'expresso' (with the RMA-advocated pre-processing methods) should be segfault-free... HTH, L. > Thanks, > > Hua Li > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >