[R] [Fwd: loading SPOT file]

[Martin Morgan]

Hi Barbara  -- ask on the Bioconductor mailing list.

   http://bioconductor.org/docs/mailList.html

Include the output of the command sessionInfo() after the failure. Be 
sure to update to a current version of R / Bioconductor, for the latter 
following 'Update installed Bioconductor packages' at

   http://bioconductor.org/docs/install

Martin

Barbara Cegielska wrote:
> 
> 
> ------------------------------------------------------------------------
> 
> Subject:
> loading SPOT file
> From:
> Barbara Cegielska <barceg at ibch.poznan.pl>
> Date:
> Wed, 06 May 2009 16:48:35 +0200
> To:
> r-help-bounces at r-project.org
> 
> To:
> r-help-bounces at r-project.org
> 
> 
> I have problem with loading SPOT files.
> 
> Sample of my operations in R object
> 
>  > fromfile=TRUE
>  > fext="spot"
>  > rawboxplot=TRUE
>  > flagi="Flags"
>  >
>  > f<-function(x) as.numeric(x$Flags > -99)
>  > targets<-readTargets("ApoAITargets.txt")
>  >
>  > if (fromfile){
> + files<-dir(pattern=fext)
> + } else {
> + dane.maTargets<-read.marrayInfo(filename=targets)
> + phenoData<-read.AnnotatedDataFrame(filename=targets)
> + files<-targets$FileName
> + }
>  >
>  >
>  > RG <- readSpot(files, as.is = TRUE, galfile="ApoAI.gal", DEBUG=FALSE, 
> skip=-1,  quote = "\"",
> + fill = TRUE)
> Error in readLines(f, n = skip + 1) : invalid 'n' argument
> 
> I would like to loead Apo.AI data from: 
> http://bioinf.wehi.edu.au/limmaGUI/DataSets.html
> 
> Thank you in advance.
> 
> Regards,
> B.
> 
> 
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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