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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