problems with marray and gpr files
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Jörg ▴ 40
@jorg-3228
Last seen 8.4 years ago
Hello, I am pretty new to marray and actually having the same problem. When using read.GenePix() I get the error ""Error in if (skip > 0) readLines(file, skip) : > missing value where TRUE/FALSE needed" Additionally I get a warning message ": In greplayout.id[1], y) : Inputstring 30 not valid with this locale." When using the skip option with the number of row in the header I get "Error in [.data.frame(dat, , info.id) : undefined columns selected" I tried different gpr files also files downloaded from: http://genomebiology.com/2003/4/2/R9/additional/ The columns are named exactly as expected in read.GenePix() so I don't think it is a problem with the files. Here they mention that it might be a problem with R locate: https://stat.ethz.ch/pipermail/bioconductor/2005-May/008928.html Unfortunately I don't know a lot about this. My System: Ubuntu Feisty Fawn, Linux 2.6.24-23-generic i686, R version 2.8.1 (also tried older versions), Bioconductor 2.3 I would be very grateful for every help or hint. thanks a lot, J?rg
marray marray • 885 views
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@martin-morgan-1513
Last seen 2 days ago
United States
J?rg <edd17 at="" gmx.de=""> writes: > Hello, > I am pretty new to marray and actually having the same problem. > When using read.GenePix() I get the error > > ""Error in if (skip > 0) readLines(file, skip) : > > missing value where TRUE/FALSE needed" > > Additionally I get a warning message > > ": In greplayout.id[1], y) : > Inputstring 30 not valid with this locale." > > When using the skip option with the number of row in the header I get > > "Error in [.data.frame(dat, , info.id) : undefined columns selected" > > > > I tried different gpr files also files downloaded from: > > http://genomebiology.com/2003/4/2/R9/additional/ > > The columns are named exactly as expected in read.GenePix() > so I don't think it is a problem with the files. > > Here they mention that it might be a problem with R locate: > https://stat.ethz.ch/pipermail/bioconductor/2005-May/008928.html > > Unfortunately I don't know a lot about this. Can you mention what the output of > sessionInfo() is? Also try > Sys.setlocale(locale="C") before read.GenePix, and if that does not work try, as you start R from the command line of your operating system, % LC_ALL="C" R It would be good if you could report back to the list whether these approaches work. Martin > My System: > > Ubuntu Feisty Fawn, Linux 2.6.24-23-generic i686, > R version 2.8.1 (also tried older versions), Bioconductor 2.3 > > > I would be very grateful for every help or hint. > > thanks a lot, > J?rg > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793

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