[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",
summary.method="avgdiff")
Hope this is useful.
Matloob
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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