Hi , We use the Bioconductor package for conversion of CEL files from affymetrix into tab-delimited (probe values to expression values).This works absolutely fine with regular arrays.(This is in Linux) For custom CDF files ,I used the "makecdfenv" package for creating the CDF files.As far as I see it the whole thing went without any warnings. But fails with a segmentation fault when executing the conversion(justRMA) On the command Line (not-Batch file) **************************************** > eset<- justRMA() Background correcting Normalizing Calculating Expression Segmentation fault **************************** In case of Batch file I get the following error #################################################### /home/ppws/intel/ppdev/R/R-1.9.1/bin/BATCH: line 55: 23075 Done ( echo "invisible(options(echo = TRUE))"; cat ${in}; echo "proc.time()" ) 23076 Segmentation fault | ${R_HOME}/bin/R ${opts} >${out} 2>&1 ############################################ I am not sure what causes this ...could you please help me on this ? Thanks for your time Chaitanya Kommidi

Could you please give the output of sessionInfo()? It looks to me that perhaps your R version (and thus probably your versions of the BioC packages) is older (basing this off the path name in your output below). It would also be helpful if you could describe a little bit better what you mean by custom CDF file. Is this for a custom array or for a regular array but you have some how modified the CDF file for your own purposes? Ben On Thu, 22 Sep 2005, Chaitanya Kommidi wrote: > Hi , > We use the Bioconductor package for conversion of CEL files from > affymetrix into tab-delimited (probe values to expression values).This > works absolutely fine with regular arrays.(This is in Linux) > > For custom CDF files ,I used the "makecdfenv" package for creating > the CDF files.As far as I see it the whole thing went without any > warnings. > But fails with a segmentation fault when executing the conversion(justRMA) > > > On the command Line (not-Batch file) > **************************************** > > eset<- justRMA() > Background correcting > Normalizing > Calculating Expression > Segmentation fault > **************************** > > In case of Batch file I get the following error > #################################################### > /home/ppws/intel/ppdev/R/R-1.9.1/bin/BATCH: line 55: 23075 > Done ( echo "invisible(options(echo = TRUE))"; cat > ${in}; echo "proc.time()" ) > 23076 Segmentation fault | ${R_HOME}/bin/R ${opts} >${out} 2>&1 > ############################################ > > > I am not sure what causes this ...could you please help me on this ? > > > Thanks for your time > > Chaitanya Kommidi > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >