The funtion read.celfile is still giving me grief in version 1.1.1 this is what I get. (Just a as a remainder some probe sets have all of their features masked). > cels<-list() > cels[1]<-"cw20001050101a.cel" > cels[2]<-"cw20001050102a.cel" > cels[3]<-"cw20001050103a.cel" > cels[4]<-"cw20001050104a.cel" > cels[5]<-"cw20001050105a.cel" > cels[6]<-"cw20001050106a.cel" > names<-list() > names[1]<-"CW20001050101A" > names[2]<-"CW20001050102A" > names[3]<-"CW20001050103A" > names[4]<-"CW20001050104A" > names[5]<-"CW20001050105A" > names[6]<-"CW20001050106A" > data <- ReadAffy(CDFfile="HG_U95Av2.CDF", CELfiles=cels, chip.names=names, rm.mask=T, verbose=F) Error in read.celfile(CELfiles[i], compress = compress.cel, sd = FALSE, : subscript out of bounds Execution halted Isaac

Dear Isaac, the error you report seems to be more in the function ReadAffy than in 'readcelfile' (according to the dump you provide). Generally, do not hesitate to send us the version number of your R installation and the platform you use.... The following is the output from an R session performed on a Linux box (Mandrake 8.2) a couple of minutes ago: > tagada <- list() > tagada[1] <- "/mnt/cdrom/LatinSquare/E_coli/000825_bgd_Ds11.CEL.gz" > tagada[2] <- "/mnt/cdrom/LatinSquare/E_coli/000825_bgd_Ds10.CEL.gz" > mynames <- c("a", "b") > p <- ReadAffy("/mnt/cdrom/LatinSquare/E_coli/1286_S01.CDF.gz", tagada, compress.cel=T, compress.cdf=T, chip.names=mynames, rm.mask=T) reading CDF file processing information reading 2 CEL files.. preparing probe level object > p Plob object CDF used=/mnt/cdrom/LatinSquare/E_coli/1286_S01.CDF.gz number of chips=2 number of genes=9842 number of probe pairs=145443 annotation= description= notes= size of chip=544x544 chip names= a b > We will look at it as soon as possible. Are the fact that all probes get 'masked' and the error in ReadAffy two different problems ? Regards, Laurent On Wed, Jun 19, 2002 at 04:26:21PM -0400, Isaac Neuhaus wrote: > The funtion read.celfile is still giving me grief in version 1.1.1 this > is what I get. (Just a as a remainder some probe sets have all of their > features masked). > > > cels<-list() > > cels[1]<-"cw20001050101a.cel" > > cels[2]<-"cw20001050102a.cel" > > cels[3]<-"cw20001050103a.cel" > > cels[4]<-"cw20001050104a.cel" > > cels[5]<-"cw20001050105a.cel" > > cels[6]<-"cw20001050106a.cel" > > names<-list() > > names[1]<-"CW20001050101A" > > names[2]<-"CW20001050102A" > > names[3]<-"CW20001050103A" > > names[4]<-"CW20001050104A" > > names[5]<-"CW20001050105A" > > names[6]<-"CW20001050106A" > > data <- ReadAffy(CDFfile="HG_U95Av2.CDF", CELfiles=cels, > chip.names=names, rm.mask=T, verbose=F) > Error in read.celfile(CELfiles[i], compress = compress.cel, sd = FALSE, > : > subscript out of bounds > Execution halted > > Isaac > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 85 http://www.cbs.dtu.dk/laurent