[BioC] Occasional seg faults in RMA

Matloob Qureshi mq2 at sanger.ac.uk
Fri Oct 31 16:53:15 MET 2003

Hi Crispin,
I've had the occasional segmentation fault using the rma() function 
too. Our rather simplistic solution was to switch to using espresso for the 
time being. It does run significantly more slowly than rma but it works ok 
for our purposes.

eset <- expresso(data, bgcorrect.method="rma",                                        
normalize.method="constant", pmcorrect.method="pmonly",                               

Hope this is useful.


On Fri, 31 Oct 2003, Crispin Miller wrote:

> Hi,
> Has anyone else experienced segmentation faults in rma()? We're still
> using R-1.7.1 and haven't upgraded bioconductor to 1.3 yet. 
> It appears to be happening during the 'Calculating Expression'  phase,
> and seems to be intermittent (I haven't been able to identify a
> pattern).
> We have written our own package with some C routines in, and I'm calling
> rma() after loading that package, but before calling any of these C
> functions (which seem to work fine anyway). 
> Am I right to assume that this is not likely to be the source of the
> problem?
> Any adivce would be most welcome!
> Thanks,
> Crispin
> Crispin Miller
> Bioinformatics Group Leader,
> The Paterson Institute For Cancer Research
> +44 161 446 3176
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