Hi, This is probably a newbie question, but I've been looking for a solution for ours. I am trying to import a SMD file (exptID=2641) into the marray package. Unfortunately this seems to fail every time: > datadir="~/Desktop" > fnames=c("28370.xls") > read.SMD(fnames=fnames, path=datadir,DEBUG=TRUE) [1] "28370.xls" Generating layout from 28370.xls [1] "Reading Gal file" [1] "done \n " Generating target sample info from all files [1] "Ch1 Intensity \\(Median\\)" Error in file(con, "r") : unable to open connection I have even tried to download the corresponding gal file from Standford, but this doesn't work either. In addition, I tried using the read.SMD2 function that somebody posted here a while ago: > read.SMD2(fnames=fnames, path=datadir,DEBUG=TRUE) [1] "~/Desktop/28370.xls" [1] NA Generating layout from 28370.xls Error in if (skip > 0) readLines(file, skip) : missing value where TRUE/FALSE needed Help! What should I do to make this thing work? Microarray and Bioconductor are new to me, but this should work, doesn't it? Kind regards, Rene Nederhand

Hi Rene What does: readLines("28370.xls") Produce? Is 28380.xls in your current working directory? Mick -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Rene Nederhand Sent: 17 March 2005 11:15 To: bioconductor@stat.math.ethz.ch Subject: [BioC] [marray] Importing SMD files into marray Hi, This is probably a newbie question, but I've been looking for a solution for ours. I am trying to import a SMD file (exptID=2641) into the marray package. Unfortunately this seems to fail every time: > datadir="~/Desktop" > fnames=c("28370.xls") > read.SMD(fnames=fnames, path=datadir,DEBUG=TRUE) [1] "28370.xls" Generating layout from 28370.xls [1] "Reading Gal file" [1] "done \n " Generating target sample info from all files [1] "Ch1 Intensity \\(Median\\)" Error in file(con, "r") : unable to open connection I have even tried to download the corresponding gal file from Standford, but this doesn't work either. In addition, I tried using the read.SMD2 function that somebody posted here a while ago: > read.SMD2(fnames=fnames, path=datadir,DEBUG=TRUE) [1] "~/Desktop/28370.xls" [1] NA Generating layout from 28370.xls Error in if (skip > 0) readLines(file, skip) : missing value where TRUE/FALSE needed Help! What should I do to make this thing work? Microarray and Bioconductor are new to me, but this should work, doesn't it? Kind regards, Rene Nederhand _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor

Hi Rene, Could you report back with the version of R and Bioconductor packages that you are using? A good way to do this is: sessionInfo() Rene Nederhand <r.nederhand@gmail.com> writes: >> datadir="~/Desktop" >> fnames=c("28370.xls") >> read.SMD(fnames=fnames, path=datadir,DEBUG=TRUE) > [1] "28370.xls" > Generating layout from 28370.xls > [1] "Reading Gal file" > [1] "done \n " > Generating target sample info from all files > [1] "Ch1 Intensity \\(Median\\)" > Error in file(con, "r") : unable to open connection A useful thing to do here is call traceback() and post the output. That can help us help you if we don't immediately recognize the error condition. The traceback() function prints out a trace of the functions that were called up until the error occurred. > In addition, I tried using the read.SMD2 function that somebody posted > here a while ago: I'm not familiar with read.SMD2, but based on the error message: >> read.SMD2(fnames=fnames, path=datadir,DEBUG=TRUE) > [1] "~/Desktop/28370.xls" > [1] NA > Generating layout from 28370.xls > Error in if (skip > 0) readLines(file, skip) : > missing value where TRUE/FALSE needed What happens if you add skip=0 to the function call? Best, + seth