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

[Naïma Oumouhou]

Thanks for your quick response

Yes I use Rgui.

I've changed the name of

"HG-U133_Plus_2_probe.tab" for  "HG-U133_Plus_2.probe.tab"

I notice that blanks appear in the mail I've send you but in my script, 
I don't have blancks in the paths « anndir » and « scmdir ».

I run R but I've got the same problem : R stops working.

So,according to your suggestions, I used RTerm and add the option 
verbose=TRUE.

Always the same problem !

I'm not sure I've used Rterm correctly.

I send you the screenshots !

Thanks for your help.

Naïma



Le 22/09/2010 22:12, cstrato a écrit :
> Dear Naima,
>
> First, your code contains the name "HG-U133_Plus_2_probe.tab", however 
> I just downloaded the file and the name is "HG-U133_Plus_2.probe_tab" 
> which must be changed to "HG-U133_Plus_2.probe.tab" (note the two dots).
>
> Second, anndir and scmdir start with " C:/...", which contains a 
> blank. I am not sure if this has an influence.
>
> I assume that you are using RGui. Please use RTerm and "verbose=TRUE" 
> which will show you the error messages you get from xps. If you still 
> get errors please send me the complete output of RTerm.
>
> Please let me know if this did solve your problem.
>
> Best regards
> Christian
> _._._._._._._._._._._._._._._._._._
> C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
> V.i.e.n.n.a           A.u.s.t.r.i.a
> e.m.a.i.l:        cstrato at aon.at
> _._._._._._._._._._._._._._._._._._
>
>
> On 9/22/10 6:31 PM, Naïma Oumouhou wrote:
>>
>>
>> Dear Christian,
>>
>> I've got an error when I want to use  import.expr.scheme() of xps 
>> package.
>>
>> I've download the CDF, annotation and probe files from the
>> AffymetrixWebsite.
>>
>> -HG-U133_Plus_2.na30.annot.csv
>>
>> -HG-U133_Plus_2.cdf
>>
>> -HG-U133_Plus_2_probe.tab
>>
>> I point libdir and anndir to the directories where the Affymetrix 
>> files are located.
>>
>>
>> library(xps)
>>
>> libdir<-"C:/Users/boubou/Desktop/Test/canc_EFS/Affy/libraryfiles"
>>
>> anndir<-" C:/Users/boubou/Desktop/Test/canc_EFS/Affy/Annotation"
>>
>> scmdir<-"
>> C:/Users/boubou/Desktop/Test/canc_EFS/Affy/CRAN/Workspaces/Schemes"
>>
>> scheme.hgu133p2.na30<-import.expr.scheme("Scheme_HGU133p2_na30",filedir=scmdir,paste(libdir,"HG-U133_Plus_2.cdf",sep="/"),paste(libdir,"HG-U133_Plus_2_probe.tab",sep="/"),paste(anndir,"HG-U133_Plus_2.na30.annot.csv",sep="/")) 
>>
>>
>> Haut du formulaire
>>
>> R stops working...I don't understand why.
>>
>> Thanks for any help!
>>
>>
>>
>> sessionInfo()
>>
>> R version 2.9.2 (2009-08-24)
>>
>> i386-pc-mingw32
>>
>> locale:
>>
>> LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 
>>
>>
>> attached base packages:
>>
>> [1] stats graphics grDevices datasets utils methods base
>>
>> other attached packages:
>>
>> [1] rcom_2.2-1 rscproxy_1.3-1
>>
>> loaded via a namespace (and not attached):
>>
>> [1] tools_2.9.2
>>
>>
>>     [[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
>>
>