[BioC] affy package and segmentation error

Robert Gentleman rgentlem at jimmy.harvard.edu
Thu Nov 4 14:59:01 CET 2004

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 
   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.


> Thanks,
> Hua Li
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> Bioconductor at 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 at jimmy.harvard.edu        |

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