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

[cstrato]

Dear Naima,

Which version of ROOT do you have installed?
Since R-2.9.2 is pretty old and requires BioC2.4, see:
http://bioconductor.org/packages/2.4/bioc/html/xps.html
you need ROOT version "root_v5.22.00.win32.vc90.msi".

Furthermore, which version of xps do you have installed?
For some reason your sessionInfo() does not mention xps.

Best regards
Christian


On 9/23/10 10:49 AM, Naïma Oumouhou wrote:
>
>
> 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]]
>>>
>>> _______________________________________________
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>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>>>
>>
>