[BioC] readGPR (arrayQuality)

[Wolfgang Huber]

Hi Tom,

you'll need to tell us more about your OS, your R version (the value of 
'version'), your locale (e.g. the result of the shell command 'locale') 
and your compile-options (the last couple of lines of config.log) in 
order to make sense of your question.

There was a similar thread not long ago,
https://stat.ethz.ch/pipermail/bioconductor/2005-May/008927.html
Perhaps it is also possible for the arrayQuality / marray people to make 
things more robust to this or have better error messages?

Best wishe
  Wolfgang



  Koonen wrote:
> Hi there,
> 
> I'm trying to do some qualitycheck on my microarray data. R seems to
> have a problem with the file.
> 
> 
>>data = readGPR(fnames = "1.1_Cy3_over_Cy5.gpr", path="/home/tom/microarray-experiment1_gpr_files/", DEBUG=TRUE)
> 
> [1] "Starting readGPR"
> [1] "/home/tom/microarray-experiment1_gpr_files/"
> [1] NA
> [1] "Reading /home/tom/microarray-experiment1_gpr_files//1.1_Cy3_over_Cy5.gpr"
> Error in readLines(con, n, ok) : invalid value for 'n'
> In addition: Warning messages:
> 1: input string 32 is invalid in this locale in: grep(pattern, x,
> ignore.case, extended, value, fixed, useBytes)
> 2: input string 32 is invalid in this locale in: grep(pattern, x,
> ignore.case, extended, value, fixed, useBytes)
> 3: input string 32 is invalid in this locale in: grep(pattern, x,
> ignore.case, extended, value, fixed, useBytes)
> 4: input string 32 is invalid in this locale in: grep(pattern, x,
> ignore.case, extended, value, fixed, useBytes)
> 5: input string 32 is invalid in this locale in: grep(pattern, x,
> ignore.case, extended, value, fixed, useBytes)
> 6: input string 32 is invalid in this locale in: grep(pattern, x,
> ignore.case, extended, value, fixed, useBytes)
> 7: input string 32 is invalid in this locale in: grep(pattern, x,
> ignore.case, extended, value, fixed, useBytes)
> 8: input string 32 is invalid in this locale in: grep(pattern, x,
> ignore.case, extended, value, fixed, useBytes)
> 9: input string 32 is invalid in this locale in: grep(pattern, x,
> ignore.case, extended, value, fixed, useBytes)
> 
> 
> Does anybody now what's the problem here?
> 
> Greetz, Tom
> 
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-- 
Best regards
   Wolfgang

-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber