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

cstrato cstrato at aon.at
Wed Sep 22 22:12:00 CEST 2010


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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