Hello Bioconductor mailing list, I have a problem: I have to read and analyse .gpr files. To read the files I used the following lines code: galinfo<- read.Galfile(?GAL.txt?,path=datadir) SigmaMir.layout <- galinfo$layout SigmaMir.gnames <- galinfo$gnames SigmaMir.targets=read.marrayInfo(file.path(datadir,?Targets.txt?)) Data<-read.GenePix(targets=SigmaMir.targets, path=datadir) but I receive an error by R: Error in if (skip > 0) readLines(file, skip) : missing value where TRUE/FALSE needed and if I made skip=FALSE in the parameters, I received the error: Error in dim(data) <- dim : attempt to set an attribute on NULL.....in fact SKIP shold be set NULL... I tried to use limma package, but I received this error:Error in `[.data.frame`(dat, , info.id) : undefined columns selected when I try to read .gpr files... I use R.6.0 .... is a problem of this version of R?? Please, help, thanx a lot! Simona Simona Rossi Research Intern Experimental Therapeutics The University of Texas M. D. Anderson Cancer Center 1515 Holcombe Blvd Houston, TX 77030 phone: (713) 745-5791 fax: (713) 745-4528 e-mail: srossi at mdanderson.org -- Email.it, the professional e-mail, gratis per te: http://www.email.it/f Sponsor: Raggruppa i tuoi finanziamenti in uno: pagherai un?unica rata fino al 50% pi? bassa della tua attuale! Clicca qui e chiedi maggiori informazioni a Prometeo! Clicca qui: http://adv.email.it/cgi- bin/foclick.cgi?mid=7433&d=20080117

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Quoting "Simo.rossi" <simo.rossi at="" email.it="">: > Hello Bioconductor mailing list, > > I have a problem: > > I have to read and analyse .gpr files. > > To read the files I used the following lines code: > > galinfo<- read.Galfile(?GAL.txt?,path=datadir) > > SigmaMir.layout <- galinfo$layout > SigmaMir.gnames <- galinfo$gnames > > SigmaMir.targets=read.marrayInfo(file.path(datadir,?Targets.txt?)) > > Data<-read.GenePix(targets=SigmaMir.targets, path=datadir) > > but I receive an error by R: > Error in if (skip > 0) readLines(file, skip) : > missing value where TRUE/FALSE needed > > > and if I made skip=FALSE in the parameters, I received the error: Error in > dim(data) <- dim : attempt to set an attribute on NULL.....in fact SKIP > shold be set NULL... > > I tried to use limma package, but I received this error:Error in > `[.data.frame`(dat, , info.id) : undefined columns selected > > when I try to read .gpr files... > > I use R.6.0 .... is a problem of this version of R?? > > Please, help, thanx a lot! Simona > > Simona Rossi > Research Intern > Experimental Therapeutics > The University of Texas M. D. Anderson Cancer Center > 1515 Holcombe Blvd > Houston, TX 77030 > phone: (713) 745-5791 > fax: (713) 745-4528 > e-mail: srossi at mdanderson.org > Hi Simona, usually when getting errors after trying to read GPR files, the "fault" is with the GPR files themselves. You can open the GPR files with Excel, for instance, and examine them: do they all have the same number of lines on the header? (having issues with the 'skip' parameter may point out to this (see ?read.table and what the 'skip' parameter does)?) Do they contain columns named the way read.gal or read.maimages expect? (check the help info for those functions to find out exactly what they expect) Do they all have the same number of rows? Sometimes, when using different character sets, a few hard to trace errors may appear, but that's more uncommon. I'd say 99% of the errors can be located by answering those questions. If the columns containing the signals (and/or background) are not named the way those functions expect, you can always explicitly indicate their names yourself (or change them in the original GPR files), etc. Sorry I can't be more specific, which I can't without looking at the files myself. I hope this helps a bit 'though. Jose -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.