

Christian,

Thanks four your response.
I've installed R 2.9.2, ROOT v5.24.00 and xps v1.8.3

I’ve tested these different configurations:

1. R 2.11.1

ROOT 5.24.00

Xps 1.8.3

  and

2. R 2.9.2

ROOT 5.22.00

Xps 1.4.10

I’ve got the same problem !I don’t know if there is a link with my 
problem but my OS is Windows vista.

My 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] xps_1.4.10 rcom_2.2-1 rscproxy_1.3-1

loaded via a namespace (and not attached):

[1] tools_2.9.2

Thanks for your help

Naïma







Le 23/09/2010 20:28, cstrato a écrit :
> 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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>>>> Search the archives:
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>>>>
>>>
>>
>


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