Dear Sally, The limma output shows that it has read all your ImaGene files correctly. I suspect that your targets file has a spurious blank line at the end of the file that you need to remove. This causes limma to try to read a non-existent file with name "". Best wishes Gordon >Date: Thu, 03 Jan 2008 11:33:24 -0800 >From: Sally <sagoldes at="" shaw.ca=""> >Subject: [BioC] Limma: Trying to read in imagene files >To: bioconductor at stat.math.ethz.ch >Message-ID: <000801c84e3f$a7ce9920$263f4518 at sghome> >Content-Type: text/plain > >I've been trying to troubleshoot this for a couple of days and can't >find the problem. I wasn't having this problem before so I don't >know what has changed. I am getting the following error message: > > > RG<-read.imagene(files,wt.fun=myfun) >Read header information >Read 215s48Cy3flagvalueschanged.txt >Read 215s48Cy5flagvalueschanged.txt >Read 225s48Cy3flagvalueschanged.txt >Read 225s48Cy5flagvalueschanged.txt >Read 234s48Cy3flagvalueschanged.txt >Read 234s48Cy5flagvalueschanged.txt >Read 196s48Cy3flagvalueschanged.txt >Read 196s48Cy5flagvalueschanged.txt >Read 199s48Cy3flagvalueschanged.txt >Read 199s48Cy5flagvalueschanged.txt >Read 217s48Cy3flagvalueschanged.txt >Read 217s48Cy5flagvalueschanged.txt >Error in if (skip > 0) readLines(file, skip) : argument is of length zero >In addition: Warning messages: >1: In file(file, "r") : > file("") only supports open = "w+" and open = "w+b": using the former >2: In readImaGeneHeader(fullname) : > End of file encountered before End Header >3: In file(file, "r") : > file("") only supports open = "w+" and open = "w+b": using the former > > > >My targets file looks like this > > SlideNumber Name FileNameCy3 FileNameCy5 Cy3 Cy5 > 215 215s48 215s48Cy3flagvalueschanged.txt > 215s48Cy5flagvalueschanged.txt infected control > 225 225s48 225s48Cy3flagvalueschanged.txt > 225s48Cy5flagvalueschanged.txt control infected > 234 234s48 234s48Cy3flagvalueschanged.txt > 234s48Cy5flagvalueschanged.txt infected control > 196 196s48 196s48Cy3flagvalueschanged.txt > 196s48Cy5flagvalueschanged.txt control infected > 199 199s48 199s48Cy3flagvalueschanged.txt > 199s48Cy5flagvalueschanged.txt infected control > 217 217s48 217s48Cy3flagvalueschanged.txt > 217s48Cy5flagvalueschanged.txt control infected > > >Thanks > >Sally