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

[cstrato]

Dear Caimiao

Although I have tested all annotation files from na21 until na25, I have 
for some reason never tested the new version na26.
Sadly, this is the first version where Affymetrix has changed the format 
of the annotation file.

Luckily, the workaround is simple:
Please delete the first 12 lines of file "HG-U133_Plus_2.na26.annot.csv" 
so that the file start with "Probe Set ID".

I have just tested that this solves the problem. In order to see that 
the annotation file has been imported correctly, you can do:
export(scheme.hgu133p2.na26, treetype="ann", 
outfile="HGU133p2_na26_ann.txt")
This will export the annotation data as text file.

Please let me know if this did solve your problem.

Since you are using xps on Windows here is one suggestion:
If you run R from Rterm on the Console, you will see all messages when 
you set "verbose=TRUE", which I would recommend.

Thank you for reporting the problem, I will update my package soon.

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]]
>>
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>>
>>
>>     
>
>
>
>