Hi Agnes, Amazing! It worked! Thank you so much. Now, do I just repeat the same thing for the other 5 files? Thanks again, Amy. ---------------------------------------------------------------------- ----- > Hi Amy, > > Did you switch your working directory to the directory containing your > gpr files? By default, read.GenePix() is looking for fnames in ".". To > switch directory, you can either do: > > datadir <- system.file("Samsfish", package = "marray") > setwd(datadir) > data <- read.GenePix(fnames="samcellINF11a.gpr") > > or > > data <- read.GenePix(fnames="samcellINF11a.gpr", path=datadir) > > I hope this will help, > > Agnes > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Amy Mikhail > Sent: Wednesday, June 29, 2005 1:22 PM > To: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] read.GenePix not opening connection > > Hi, > > Unfortunately there are more error messages; > >> data <- read.GenePix(fnames=SamsfishTargets$FileName) > Error in file(con, "r") : unable to open connection > In addition: Warning message: > cannot open file './NA' > > and for the next one... > >> data <- read.GenePix(fnames="samcellINF11a.gpr") > Error in file(con, "r") : unable to open connection > In addition: Warning message: > cannot open file './samcellINF11a.gpr' > > Cheers, > Amy. > > P.s., just a thought but when I had a look in the .gpr files with > notepad > they specified the path for the gal file as: > > ATF 1.0 > 29 56 > "Type=GenePix Results 3" > "DateTime=2005/05/09 09:18:06" > "Settings=" > "GalFile=D:\My Documents\sam\salmonid seq database\Grasp > arrays\16kGAL_txt.gal" > > ...which is where it is stored on the GenePix computer, not the one I'm > currently working from... > > Could this be the problem? > > > -------------------------------------------------------------------- ---- > --- >> Hmmm. I have never *just* used the targets argument. >> >> What happens when you try: >> >> data <- read.GenePix(fnames=SamsfishTargets$FileName) >> >> or >> >> data <- read.GenePix(fnames="samcellINF11a.gpr") >> >> ?? >> >> >> >> -----Original Message----- >> From: bioconductor-bounces at stat.math.ethz.ch on behalf of Amy Mikhail >> Sent: Wed 29/06/2005 8:51 PM >> To: bioconductor at stat.math.ethz.ch >> Cc: >> Subject: Re: [BioC] read.GenePix not opening connection >> >> Hi, >> >> Code is below: >> >>> library(marray) >>> dir(system.file("Samsfish", package = "marray")) >> [1] "16kGAL.gal" "fishData.txt" "samcellINF10b.gpr" >> [4] "samcellINF11a.gpr" "samcellINF12a.gpr" "samcellINF7a.gpr" >> [7] "samcellINF8a.gpr" "samcellINF9a.gpr" >>> datadir <- system.file("Samsfish", package = "marray") >>> SamsfishTargets <- read.marrayInfo(file.path(datadir, > "fishData.txt")) >> data <- read.GenePix(targets=SamsfishTargets) >> Error in file(con, "r") : unable to open connection >> In addition: Warning message: >> cannot open file './samcellINF8a.gpr' >>> ?read.GenePix >>> data <- read.GenePix(targets=SamsfishTargets) >> Error in file(con, "r") : unable to open connection >> In addition: Warning message: >> cannot open file './samcellINF8a.gpr' >> >> The contents of fishData.txt reads: >> >> fileName slideNumber >> 1 samcellINF7a.gpr 1 >> 2 samcellINF8a.gpr 2 >> 3 samcellINF9a.gpr 3 >> 4 samcellINF10b.gpr 4 >> 5 samcellINF11a.gpr 5 >> 6 samcellINF12a.gpr 6 >> >> (spaces are tabs). >> >> So, what have I done wrong? >> >> Cheers, >> Amy. >> >> > -------------------------------------------------------------------- ---- > --- >>> Please post all your code, including the contents of whatever file > you >> read into SamsfishTargets. >>> >>> The error you are getting is because R cannot find the files you are >> telling it to open. 99.999999999% of the time this is user error :-) >>> >>> Mick >>> >>> >>> >>> -----Original Message----- >>> From: bioconductor-bounces at stat.math.ethz.ch on behalf of Amy > Mikhail >> Sent: Wed 29/06/2005 8:34 PM >>> To: bioconductor at stat.math.ethz.ch >>> Cc: >>> Subject: [BioC] read.GenePix not opening connection >>> >>> Hi, >>> >>> I am new to microarray analysis and have been trying to use marray > (in R >> 2.1.0) to read in data from GenePix (.gpr) files, but it hasn't >> worked... >>> >>> There are 6 .gpr files (e.g. samcellINF8a.gpr as below), the sample >> description .txt file and a .gal file in my directory (folder > containing >> files is called Samsfish). I've been trying to copy the example in > the >> vignette entittled "Quick Start Guide for marray". It worked fine up >> until the following line of code: >>> >>>> data <- read.GenePix(targets=SamsfishTargets) >>> >>> ...which gives me this error message: >>> >>> Error in file(con, "r") : unable to open connection >>> In addition: Warning message: >>> cannot open file './samcellINF8a.gpr' >>> >>> (or variations on a theme) >>> >>> Do you know what this means? >>> >>> What can I do about it? >>> >>> Many thanks, >>> Amy >>> >>> >>> >>> ------------------------------------------- >>> Amy Mikhail >>> Research student >>> University of Aberdeen >>> Zoology Building >>> Tillydrone Avenue >>> Aberdeen AB24 2TZ >>> Scotland >>> Email: a.mikhail at abdn.ac.uk >>> Phone: 00-44-1224-272880 (lab) >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> >>> >>> >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > >