Hell everyone! I am trying to do single-channel normalization for my serverl slides using limma. After I read the userguide of limma, I made a Targets file.It is just like: SlideNumber FileName Cy3 Cy5 1 2004-4-2-cy3(450)-0409-Con-only532.gpr Con Blank 2 2004-4-2-cy3(450)-0410-A24h-only532.gpr A1h Blank 3 2004-4-2-cy3(450)-4526-A5h-only532.gpr A5h Blank 4 2004-4-2-cy3(450)-4527-A10h-only532.gpr A10h Blank 5 2004-4-2-cy3(450)-4529-A1h-only532.gpr A24h Blank And the file's name is Targets.I put it with the five *.gpr under the same directory of limma's data. But I failed in running limma.This is the result: > targets <- readTargets() Error in file(file, "r") : unable to open connection In addition: Warning message: cannot open file `Targets.txt' Could anyone tell me why? Thank you very much! -- Xiaopeng ZHANG <xpzhang@genetics.ac.cn>

Hi, On Mon, 14 Jun 2004, xpzhang wrote: > using limma. After I read the userguide of limma, I made a Targets > file.It is just like: > SlideNumber FileName Cy3 Cy5 > 1 2004-4-2-cy3(450)-0409-Con-only532.gpr Con Blank > 2 2004-4-2-cy3(450)-0410-A24h-only532.gpr A1h Blank ... <snip> > And the file's name is Targets. Do you mean "Targets.txt"? If in doubt about whether limma is accessing the correct file, specify the full filename as an argument to readTargets, e.g. readTargets("MyTargetsFile.txt") See ?readTargets for more information. > But I failed in running limma.This is the result: > > targets <- readTargets() > Error in file(file, "r") : unable to open connection It certainly sounds like limma cannot find your file. Check your current working directory in R, using getwd(). Check that your targets file is in that directory and that it is called "Targets.txt", or whatever you specify for the file argument of readTargets. (See ?readTargets). If you still have trouble, check that your targets file is tab-delimited (not space-delimited) and that there are no extra tabs at the end of rows. You could also try removing the special characters from your gpr filenames, e.g. the parentheses: '(' and ')' but this shouldn't really be necessary. Regards, James