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",filedi r=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]]

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, Na?ma 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",file dir=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_MONETAR Y=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 >

Dear Naima, Now I understand the problem. Sadly, xps works only with WinXP, see: https://www.stat.math.ethz.ch/pipermail/bioconductor/2009-December/030 783.html Best regards Christian On 9/24/10 10:31 AM, Na?ma 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_MONETAR Y=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 > > Na?ma > > > > > > > > Le 23/09/2010 20:28, cstrato a ?crit : >> 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, Na?ma 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. >>> >>> Na?ma >>> >>> >>> >>> Le 22/09/2010 22:12, cstrato a ?crit : >>>> 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, Na?ma 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_MON ETARY=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 >>>>> >>>> >>> >> >