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

[cstrato]

Dear Caimiao

This is really strange, I will investigate and let you know.

Best regards
Christian


Wei,Caimiao wrote:
> 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
>>
>>
>>
>>       [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>
>>
>>     
>
>
>
>