Hello, I am trying to read a batch of delimited-tab text files into marray package. Somehow I kept getting error message like: >Data=read.marrayRaw(fnames=fnames,name.Rf="Spot Median Intensity Cy5",name.Gf="Spot Median Intensity Cy3",name.Rb="Background Median Intensity Cy5",name.Gb="Background Median Intensity Cy3",gnames="Clone ID",sep="\t") Reading ... ./chip1.txt Reading ... ./chip2.txt Error in if (skip > 0) readLines(file, skip) : missing value where TRUE/FALSE needed Would anyone help me to figure out what my problem is? Thanks a lot! Really appreciate your help! Yanqin --------------------------------- --------------------------------- [[alternative HTML version deleted]]

Hi Yanqin, Assuming you have no header infomration you want to skip, can you try the following command strsplit(readLines(fnames[1], n=1), split="\t") and check if you enter the name of the columns correctly in the argument. You can also add skip = 0 in the call and see if it works. Cheers YH On Tue, 15 Mar 2005, Yanqin Yang wrote: > Hello, > > > I am trying to read a batch of delimited-tab text files into marray package. > Somehow I kept getting error message like: > > >Data=read.marrayRaw(fnames=fnames,name.Rf="Spot Median Intensity Cy5",name.Gf="Spot Median Intensity Cy3",name.Rb="Background Median Intensity Cy5",name.Gb="Background Median Intensity Cy3",gnames="Clone ID",sep="\t") > > > Reading ... ./chip1.txt > Reading ... ./chip2.txt > Error in if (skip > 0) readLines(file, skip) : missing value where TRUE/FALSE needed > > > Would anyone help me to figure out what my problem is? > > > Thanks a lot! Really appreciate your help! > > Yanqin > > > > > > > --------------------------------- > > > > > > > --------------------------------- > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

Hi Yanqin, Yanqin Yang <yanqin_yang@yahoo.com> writes: > Thanks so much for kindly help! Here is the output according to your suggestions. > >> traceback() > 2: read.table(f, skip = skip2, header = TRUE, sep = sep, as.is = TRUE, > quote = quote, check.names = FALSE, comment.char = "", nrows = nspots, > ...) > 1: read.marrayRaw(fnames = fnames, name.Rf = "Spot Mean Intensity (Cy5_39)", > name.Gf = "Spot Mean Intensity (Cy3_34)", name.Rb = "Background Median Intensity > (Cy5_39)", > name.Gb = "Background Median Intensity (Cy3_34)", gnames = "Clone ID", > sep = " ") >> sessionInfo() > R version 2.0.0, 2004-10-04, i386-pc-mingw32 > attached base packages: > [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" "base" > other attached packages: > marray limma > "1.5.25" "1.8.18" > I still couldn't figure out the solution of my erro message: Error in if (skip > 0) > readLines(file, skip) : missing value where TRUE/FALSE needed The error message seems to be saying that the skip parameter is missing or NA and it needs to have a value >= 0. So you could try specifying that. You could also try setting DEBUG=TRUE and see if that helps you to diagnose the problem. + seth