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

[cstrato]

Dear Naima,

Now I understand the problem. Sadly, xps works only with WinXP, see:
https://www.stat.math.ethz.ch/pipermail/bioconductor/2009-December/030783.html

Best regards
Christian


On 9/24/10 10:31 AM, Naïma Oumouhou wrote:
>
>
> 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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>>>>>
>>>>
>>>
>>
>