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 -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}

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 > > -------------------------------------------------------- > > > This email is confidential and intended solely for the use o...{{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >