[BioC] Package "xps" "import.expr.scheme" error

[Wei,Caimiao]

Dear Christian,

[1]. Yes, I did download the three files from Affymetrix website.

[2]. yes, these files are placed in the directories I specified in the code line.

[3]. I first used "HG-U133_Plus_2.probe.tab"
then I changed "HG-U133_Plus_2_probe_tab" to "HG-U133_Plus_2_probe.tab", the error is still the same.


Caimiao
-----Original Message-----
From: cstrato [mailto:cstrato at aon.at]
Sent: Thursday, October 23, 2008 10:38 AM
To: Wei,Caimiao
Cc: Bioconductor mailing list
Subject: Re: [BioC] Package "xps" "import.expr.scheme" error

Dear Caimiao

Since you are showing a code fragment from my sample script I am not
quite sure what you did.
Did you download the CDF, annotation and probe files from the Affymetrix
website?
Did you point libdir and anndir to the directories where the Affymetrix
files are located?
Did you change the name of the downloaded file
"HG-U133_Plus_2_probe_tab" to "HG-U133_Plus_2_probe.tab"?
(I am not sure if "HG-U133_Plus_2.probe.tab" will work)

Please let me know if this solved your problem.

Best regards
Christian


Wei,Caimiao wrote:
> I am importing chip definition and annotation files to create a ROOT scheme and get this error:
>
> Error in import.expr.scheme(filename = "Scheme_HGU133p2_na26", filedir = scmdir,  :
>   error in function 'ImportExprSchemes'
>
>
>> libdir <- "/mypath/Affy/libraryfiles"
>> anndir <- "/mypath/Affy/Annotation"
>> scmdir <- "/mypath/CRAN/Workspaces/Schemes"
>>
>> scheme.hgu133p2.na26 <- import.expr.scheme(filename="Scheme_HGU133p2_na26",
>>
> + filedir=scmdir,schemefile=paste(libdir,"HG-U133_Plus_2.cdf",sep="/"),
> + probefile=paste(libdir,"HG-U133_Plus_2.probe.tab",sep="/"),
> +  annotfile=paste(anndir,"HG-U133_Plus_2.na26.annot.csv",sep="/"))
>
> Error in import.expr.scheme(filename = "Scheme_HGU133p2_na26", filedir = scmdir,  :
>   error in function 'ImportExprSchemes'
>
>
>
>> sessionInfo()
>>
> R version 2.7.2 (2008-08-25)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] xps_1.0.2
>
>
> Thanks for any help!
>
> Caimiao
>
>
>
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