[BioC] error in import.exon.scheme, XPS package

[Henrik Bengtsson]

Don't use paste() to create you pathnames.  Instead, use file.path(),
which takes care of all this for you.

/Henrik

On Thu, Apr 8, 2010 at 8:28 PM, cstrato <cstrato at aon.at> wrote:
> Dear Lisa,
>
> Could you please supply the sessionInfo() and the ROOT version you use?
>
> From your code I assume that you are using WinXP.
>
> I am not sure if paste(...,sep="\\") is allowed, thus could you please try
> paste(...,sep="/") and:
> libdir <- "C:/home/pathto/Affy/libraryfiles"
> anndir <- "C:/home/pathto/Affy/Annotation"
> etc
> From within R it is not necessary to use "\" on WinXP, you can use "/" as on
> Unix.
>
> Could you please run the code again from RTerm and send me the complete
> output.
>
> Best regards
> Christian
>
>
> Lisa Mu wrote:
>>
>> Dear Christian:
>>
>> I am new to XPS and  following your paper on comparing XPS with APT.
>>
>> I used the listed code to create scheme object:
>>
>> Scheme.HuEx10stv2r2.na27=import.exon.scheme( filename   =
>> "Scheme_HuEx10stv2r2_na27",
>>
>>  filedir    = scmdir,
>>
>> layoutfile = paste(libdir, "HuEx-1_0-st-v2.r2.clf", sep = "\\"),
>>
>> schemefile = paste(libdir, "HuEx-1_0-st-v2.r2.pgf", sep = "\\"),
>>
>>  probeset   = paste(anndir, "HuEx-1_0-st-na27.hg18.probeset.csv", sep =
>> "\\"),
>>
>>  transcript = paste(anndir, "HuEx-1_0-st-v2.na27.hg18.transcript.csv", sep
>> =
>> "\\"),
>>
>> add.mask=FALSE ,
>>
>> verbose=TRUE  )
>>
>> And I got error message :   Error in import.exon.scheme(filename =
>> "Scheme_HuEx10stv2r2_na27", filedir = scmdir,  :
>>  error in function ‘ImportExonSchemes’
>>
>> I am wondering whether you could give any suggestion on this.
>>
>> Thanks a lot.
>>
>> Lisa
>>
>>        [[alternative HTML version deleted]]
>>
>>  ------------------------------------------------------------------------
>>
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>
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