[BioC] problems with marray and gpr files

J.delasHeras at ed.ac.uk J.delasHeras at ed.ac.uk
Thu Jan 17 13:06:42 CET 2008

Quoting "Simo.rossi" <simo.rossi at email.it>:

> Hello Bioconductor mailing list,
>     I have a problem:
> I have to read and analyse .gpr files.
> To read the files I used the following lines code:
> galinfo<- read.Galfile(“GAL.txt”,path=datadir)
> SigmaMir.layout <- galinfo$layout
> SigmaMir.gnames <- galinfo$gnames
> SigmaMir.targets=read.marrayInfo(file.path(datadir,”Targets.txt”))
> Data<-read.GenePix(targets=SigmaMir.targets, path=datadir)
> but I receive an error by R:
> Error in if (skip > 0) readLines(file, skip) :
>   missing value where TRUE/FALSE needed
> and if I made skip=FALSE in the parameters, I received the error: Error in
> dim(data) <- dim : attempt to set an attribute on NULL.....in fact SKIP
> shold be set NULL...
> I tried to use limma package, but I received this error:Error in
> `[.data.frame`(dat, , info.id) : undefined columns selected
> when I try to read .gpr files...
> I use R.6.0 .... is a problem of this version of R??
> Please, help, thanx a lot! Simona
> Simona Rossi
> Research Intern
> Experimental Therapeutics
> The University of Texas M. D. Anderson Cancer Center
> 1515 Holcombe Blvd
> Houston, TX 77030
> phone: (713) 745-5791
> fax: (713) 745-4528
> e-mail: srossi at mdanderson.org

Hi Simona,

usually when getting errors after trying to read GPR files, the  
"fault" is with the GPR files themselves.
You can open the GPR files with Excel, for instance, and examine them:
do they all have the same number of lines on the header? (having  
issues with the 'skip' parameter may point out to this (see  
?read.table and what the 'skip' parameter does)?)
Do they contain columns named the way read.gal or read.maimages  
expect? (check the help info for those functions to find out exactly  
what they expect)
Do they all have the same number of rows?
Sometimes, when using different character sets, a few hard to trace  
errors may appear, but that's more uncommon.

I'd say 99% of the errors can be located by answering those questions.  
If the columns containing the signals (and/or background) are not  
named the way those functions expect, you can always explicitly  
indicate their names yourself (or change them in the original GPR  
files), etc.

Sorry I can't be more specific, which I can't without looking at the  
files myself. I hope this helps a bit 'though.


Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
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University of Edinburgh
Edinburgh EH9 3JR

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