FW: XPS crahses R session
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cstrato ★ 3.9k
@cstrato-908
Last seen 6.2 years ago
Austria
Dear Guido, Since Bioconductor has compiled the Windows version of xps using root 5.22.00 you need to install the binary of this version, as mentioned in "System Requirements". You can download this version from: http://root.cern.ch/root/Version522.html I would suggest to install version: root_v5.22.00.win32.vc90.msi Please see also my introductory comments for Windows users: https://www.stat.math.ethz.ch/pipermail/bioconductor/2008-December/025 452.html Please let me know if this solved your problem. Best regards Christian P.S.: Although the BioC mailing list is currently down I assume that it will contain your question, thus I cc to the list. Hooiveld, Guido wrote: > > Hi, > Since the BioC mailing list seems not to work properly (i haven't > received any BioC mails the last days), I am sending you this email > directly. > > Regards, > Guido > > ------------------------------------------------ > Guido Hooiveld, PhD > Nutrition, Metabolism & Genomics Group > Division of Human Nutrition > Wageningen University > Biotechnion, Bomenweg 2 > NL-6703 HD Wageningen > the Netherlands > tel: (+)31 317 485788 > fax: (+)31 317 483342 > internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/> > email: guido.hooiveld at wur.nl > > > > -------------------------------------------------------------------- ---- > *From:* Hooiveld, Guido > *Sent:* 17 August 2009 17:50 > *To:* bioconductor at stat.math.ethz.ch > *Subject:* XPS crahses R session > > Dear Christian, > > I am new to XPS and i would like to use it to analyse Mouse Gene ST > arrays (MoGene ST arrays). However, XPS crashes my R session when > trying to create a ROOT scheme file fore these arrays, and i don't > know what may go wrong. Hopefully you can advise. :) > > Thanks, > Guido > > > What did i do? > - I am using a windows machine (WinXP-SP3, 4GB memory) > - I installed ROOT v5.24.00 (1st) and XPS (2nd). PS: is there a way to > check whether ROOT installed properly? > - Then i downloaded the 'library' files', MoGene-1_0-st-v1.r4.pgf and > MoGene-1_0-st-v1.r4.clf, and put them in a directory > (D:\XPS\Affy\libraryfiles) > - Next i downloaded the latest annotation files from Affymetrix > (MoGene-1_0-st-v1.na29.mm9.transcript.csv and > MoGene-1_0-st-v1.na29.mm9.probeset.csv), and repaired them according > to your instructions here: > http://article.gmane.org/gmane.science.biology.informatics.conductor /24587. > The annotation files are in the dir D:\XPS\Affy\Annotation. > - I also created a dir to save the ROOT scheme > file (D:\XPS\CRAN\Workspaces\Schemes). > > When running XPS to create the scheme file R crashes... > > My lines of code: > library(xps) > libdir <- "d:/XPS/Affy/libraryfiles" > anndir <- "d:/XPS/Affy/Annotation" > scmdir <- "d:/XPS/CRAN/Workspaces/Schemes" > Below it crashes (line is from your previous referred post on the > mailing list): > > scheme.mogene10stv1r4.na29 <- > import.exon.scheme("Scheme_MoGene10stv1r4_na29",filedir=scmdir, > paste(libdir,"MoGene-1_0-st-v1.r4.clf",sep="/"), > paste(libdir,"MoGene-1_0-st-v1.r4.pgf",sep="/"), > paste(anndir,"MoGene- 1_0-st-v1.na29.mm9.probeset.fixed.csv",sep="/"), > paste(anndir,"MoGene- 1_0-st-v1.na29.mm9.transcript.fixed.csv",sep="/")) > > Error message: > Rgui.exe - Application error. The instruction at "0x002288931" > references memory at "0x8d5056fc". The memory could not be "read". > > > > sessionInfo() > R version 2.9.0 (2009-04-17) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] xps_1.4.8 > > > > > > > ------------------------------------------------ > Guido Hooiveld, PhD > Nutrition, Metabolism & Genomics Group > Division of Human Nutrition > Wageningen University > Biotechnion, Bomenweg 2 > NL-6703 HD Wageningen > the Netherlands > tel: (+)31 317 485788 > fax: (+)31 317 483342 > internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/> > email: guido.hooiveld at wur.nl > >
Annotation GO xps Annotation GO xps • 1.1k views
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Guido Hooiveld ★ 4.1k
@guido-hooiveld-2020
Last seen 4 days ago
Wageningen University, Wageningen, the …
Hi Christian, Indeed, downgrading to v5.22.00 of ROOT solved the problem I had (I initially had the impression the version of ROOT should _at least_ be v5.22). XPS is now working fine. Still one question though, if I would like to calculate the expression values of all 35519 probesets that are on the MoGene ST array (as are e.g. visible in the Affy's NetAffx annotation file and the GEO platform entry @ NCBI [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6246]), how to set the argument 'exonlevel'? If I set it @ 'all', then expression estimates of only 28837 probesets are returned. With 'metacore+affx' this number is (reduced to) 25690. Thanks, Guido > library(xps) Welcome to xps version 1.4.8 an R wrapper for XPS - eXpression Profiling System (c) Copyright 2001-2009 by Christian Stratowa > libdir <- "d:/XPS/Affy/libraryfiles" > anndir <- "d:/XPS/Affy/Annotation" > scmdir <- "d:/XPS/CRAN/Workspaces/Schemes" > celdir <- "d:/XPS/ChipData/Gene/Linda" > datdir <- "d:/XPS/CRAN/Workspaces/ROOTData" > scheme.mogene10stv1r4.na29 <- import.exon.scheme("Scheme_MoGene10stv1r4_na29",filedir=scmdir, paste(libdir,"MoGene-1_0-st-v1.r4.clf",sep="/"), paste(libdir,"MoGene-1_0-st-v1.r4.pgf",sep="/"), paste(anndir,"MoGene-1_0-st-v1.na29.mm9.probeset.fixed.csv",sep="/"), paste(anndir,"MoGene- 1_0-st-v1.na29.mm9.transcript.fixed.csv",sep="/")) > scheme.MoGene <- root.scheme(paste(scmdir,"Scheme_MoGene10stv1r4_na29.root",sep="/")) > data.linda <- root.data(scheme.MoGene, paste(datdir,"MoGene_Linda_cel.root",sep="/")) > data.rma <- rma(data.linda,"MoGene_Linda_RMA",filedir=datdir,tmpdir="",background= "a ntigenomic",normalize=TRUE,exonlevel="metacore+affx",verbose=TRUE) > data.rma <- rma(data.linda,"MoGene_Linda_RMA2",filedir=datdir,tmpdir="",background =" antigenomic",normalize=TRUE,exonlevel="all",verbose=TRUE) > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of cstrato > Sent: 17 August 2009 20:13 > To: Hooiveld, Guido; Bioconductor > Subject: Re: [BioC] FW: XPS crahses R session > > Dear Guido, > > Since Bioconductor has compiled the Windows version of xps > using root 5.22.00 you need to install the binary of this > version, as mentioned in "System Requirements". You can > download this version from: > http://root.cern.ch/root/Version522.html > I would suggest to install version: root_v5.22.00.win32.vc90.msi > > Please see also my introductory comments for Windows users: > https://www.stat.math.ethz.ch/pipermail/bioconductor/2008-Dece > mber/025452.html > > > Please let me know if this solved your problem. > > Best regards > Christian > > P.S.: Although the BioC mailing list is currently down I > assume that it will contain your question, thus I cc to the list. > > Hooiveld, Guido wrote: > > > > Hi, > > Since the BioC mailing list seems not to work properly (i haven't > > received any BioC mails the last days), I am sending you this email > > directly. > > > > Regards, > > Guido > > > > ------------------------------------------------ > > Guido Hooiveld, PhD > > Nutrition, Metabolism & Genomics Group Division of Human Nutrition > > Wageningen University Biotechnion, Bomenweg 2 > > NL-6703 HD Wageningen > > the Netherlands > > tel: (+)31 317 485788 > > fax: (+)31 317 483342 > > internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/> > > email: guido.hooiveld at wur.nl > > > > > > > > > ---------------------------------------------------------------------- > > -- > > *From:* Hooiveld, Guido > > *Sent:* 17 August 2009 17:50 > > *To:* bioconductor at stat.math.ethz.ch > > *Subject:* XPS crahses R session > > > > Dear Christian, > > > > I am new to XPS and i would like to use it to analyse Mouse Gene ST > > arrays (MoGene ST arrays). However, XPS crashes my R session when > > trying to create a ROOT scheme file fore these arrays, and i don't > > know what may go wrong. Hopefully you can advise. :) > > > > Thanks, > > Guido > > > > > > What did i do? > > - I am using a windows machine (WinXP-SP3, 4GB memory) > > - I installed ROOT v5.24.00 (1st) and XPS (2nd). PS: is > there a way to > > check whether ROOT installed properly? > > - Then i downloaded the 'library' files', > MoGene-1_0-st-v1.r4.pgf and > > MoGene-1_0-st-v1.r4.clf, and put them in a directory > > (D:\XPS\Affy\libraryfiles) > > - Next i downloaded the latest annotation files from Affymetrix > > (MoGene-1_0-st-v1.na29.mm9.transcript.csv and > > MoGene-1_0-st-v1.na29.mm9.probeset.csv), and repaired them > according > > to your instructions here: > > > http://article.gmane.org/gmane.science.biology.informatics.con > ductor/24587. > > The annotation files are in the dir D:\XPS\Affy\Annotation. > > - I also created a dir to save the ROOT scheme file > > (D:\XPS\CRAN\Workspaces\Schemes). > > > > When running XPS to create the scheme file R crashes... > > > > My lines of code: > > library(xps) > > libdir <- "d:/XPS/Affy/libraryfiles" > > anndir <- "d:/XPS/Affy/Annotation" > > scmdir <- "d:/XPS/CRAN/Workspaces/Schemes" > > Below it crashes (line is from your previous referred post on the > > mailing list): > > > > scheme.mogene10stv1r4.na29 <- > > import.exon.scheme("Scheme_MoGene10stv1r4_na29",filedir=scmdir, > > paste(libdir,"MoGene-1_0-st-v1.r4.clf",sep="/"), > > paste(libdir,"MoGene-1_0-st-v1.r4.pgf",sep="/"), > > > paste(anndir,"MoGene- 1_0-st-v1.na29.mm9.probeset.fixed.csv",sep="/"), > > > paste(anndir,"MoGene- 1_0-st-v1.na29.mm9.transcript.fixed.csv",sep="/") > > ) > > > > Error message: > > Rgui.exe - Application error. The instruction at "0x002288931" > > references memory at "0x8d5056fc". The memory could not be "read". > > > > > > > sessionInfo() > > R version 2.9.0 (2009-04-17) > > i386-pc-mingw32 > > > > locale: > > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > > Kingdom.1252;LC_MONETARY=English_United > > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets > methods base > > > > other attached packages: > > [1] xps_1.4.8 > > > > > > > > > > > > > ------------------------------------------------ > > Guido Hooiveld, PhD > > Nutrition, Metabolism & Genomics Group Division of Human Nutrition > > Wageningen University Biotechnion, Bomenweg 2 > > NL-6703 HD Wageningen > > the Netherlands > > tel: (+)31 317 485788 > > fax: (+)31 317 483342 > > internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/> > > email: guido.hooiveld at wur.nl > > > > > > _______________________________________________ > 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 > >
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Dear Guido, Please have a look at the help file "?exonLevel". You will see that setting exonlevel=c(992316,992316,992316) will create expression levels for all 35518 (35519 - 1AFFX) probesets. However, I do not recommend this since I believe that adding exon+intron+antigenomic probesets will only add noise to the results. Best regards Christian Hooiveld, Guido wrote: > Hi Christian, > > Indeed, downgrading to v5.22.00 of ROOT solved the problem I had (I > initially had the impression the version of ROOT should _at least_ be > v5.22). XPS is now working fine. > > Still one question though, if I would like to calculate the expression > values of all 35519 probesets that are on the MoGene ST array (as are > e.g. visible in the Affy's NetAffx annotation file and the GEO platform > entry @ NCBI > [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6246]), how to set > the argument 'exonlevel'? > If I set it @ 'all', then expression estimates of only 28837 probesets > are returned. With 'metacore+affx' this number is (reduced to) 25690. > > Thanks, > Guido > > > > >> library(xps) >> > > Welcome to xps version 1.4.8 > an R wrapper for XPS - eXpression Profiling System > (c) Copyright 2001-2009 by Christian Stratowa > > >> libdir <- "d:/XPS/Affy/libraryfiles" >> anndir <- "d:/XPS/Affy/Annotation" >> scmdir <- "d:/XPS/CRAN/Workspaces/Schemes" >> celdir <- "d:/XPS/ChipData/Gene/Linda" >> datdir <- "d:/XPS/CRAN/Workspaces/ROOTData" >> > > >> scheme.mogene10stv1r4.na29 <- >> > import.exon.scheme("Scheme_MoGene10stv1r4_na29",filedir=scmdir, > > paste(libdir,"MoGene-1_0-st-v1.r4.clf",sep="/"), > > paste(libdir,"MoGene-1_0-st-v1.r4.pgf",sep="/"), > > paste(anndir,"MoGene- 1_0-st-v1.na29.mm9.probeset.fixed.csv",sep="/"), > > paste(anndir,"MoGene- 1_0-st-v1.na29.mm9.transcript.fixed.csv",sep="/")) > >> scheme.MoGene <- >> > root.scheme(paste(scmdir,"Scheme_MoGene10stv1r4_na29.root",sep="/")) > >> data.linda <- root.data(scheme.MoGene, >> > paste(datdir,"MoGene_Linda_cel.root",sep="/")) > >> data.rma <- >> > rma(data.linda,"MoGene_Linda_RMA",filedir=datdir,tmpdir="",backgroun d="a > ntigenomic",normalize=TRUE,exonlevel="metacore+affx",verbose=TRUE) > >> data.rma <- >> > rma(data.linda,"MoGene_Linda_RMA2",filedir=datdir,tmpdir="",backgrou nd=" > antigenomic",normalize=TRUE,exonlevel="all",verbose=TRUE) > > > > > >> -----Original Message----- >> From: bioconductor-bounces at stat.math.ethz.ch >> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of cstrato >> Sent: 17 August 2009 20:13 >> To: Hooiveld, Guido; Bioconductor >> Subject: Re: [BioC] FW: XPS crahses R session >> >> Dear Guido, >> >> Since Bioconductor has compiled the Windows version of xps >> using root 5.22.00 you need to install the binary of this >> version, as mentioned in "System Requirements". You can >> download this version from: >> http://root.cern.ch/root/Version522.html >> I would suggest to install version: root_v5.22.00.win32.vc90.msi >> >> Please see also my introductory comments for Windows users: >> https://www.stat.math.ethz.ch/pipermail/bioconductor/2008-Dece >> mber/025452.html >> >> >> Please let me know if this solved your problem. >> >> Best regards >> Christian >> >> P.S.: Although the BioC mailing list is currently down I >> assume that it will contain your question, thus I cc to the list. >> >> Hooiveld, Guido wrote: >> >>> >>> Hi, >>> Since the BioC mailing list seems not to work properly (i haven't >>> received any BioC mails the last days), I am sending you this email >>> directly. >>> >>> Regards, >>> Guido >>> >>> ------------------------------------------------ >>> Guido Hooiveld, PhD >>> Nutrition, Metabolism & Genomics Group Division of Human Nutrition >>> Wageningen University Biotechnion, Bomenweg 2 >>> NL-6703 HD Wageningen >>> the Netherlands >>> tel: (+)31 317 485788 >>> fax: (+)31 317 483342 >>> internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/> >>> email: guido.hooiveld at wur.nl >>> >>> >>> >>> >>> >> ---------------------------------------------------------------------- >> >>> -- >>> *From:* Hooiveld, Guido >>> *Sent:* 17 August 2009 17:50 >>> *To:* bioconductor at stat.math.ethz.ch >>> *Subject:* XPS crahses R session >>> >>> Dear Christian, >>> >>> I am new to XPS and i would like to use it to analyse Mouse Gene ST >>> arrays (MoGene ST arrays). However, XPS crashes my R session when >>> trying to create a ROOT scheme file fore these arrays, and i don't >>> know what may go wrong. Hopefully you can advise. :) >>> >>> Thanks, >>> Guido >>> >>> >>> What did i do? >>> - I am using a windows machine (WinXP-SP3, 4GB memory) >>> - I installed ROOT v5.24.00 (1st) and XPS (2nd). PS: is >>> >> there a way to >> >>> check whether ROOT installed properly? >>> - Then i downloaded the 'library' files', >>> >> MoGene-1_0-st-v1.r4.pgf and >> >>> MoGene-1_0-st-v1.r4.clf, and put them in a directory >>> (D:\XPS\Affy\libraryfiles) >>> - Next i downloaded the latest annotation files from Affymetrix >>> (MoGene-1_0-st-v1.na29.mm9.transcript.csv and >>> MoGene-1_0-st-v1.na29.mm9.probeset.csv), and repaired them >>> >> according >> >>> to your instructions here: >>> >>> >> http://article.gmane.org/gmane.science.biology.informatics.con >> ductor/24587. >> >>> The annotation files are in the dir D:\XPS\Affy\Annotation. >>> - I also created a dir to save the ROOT scheme file >>> (D:\XPS\CRAN\Workspaces\Schemes). >>> >>> When running XPS to create the scheme file R crashes... >>> >>> My lines of code: >>> library(xps) >>> libdir <- "d:/XPS/Affy/libraryfiles" >>> anndir <- "d:/XPS/Affy/Annotation" >>> scmdir <- "d:/XPS/CRAN/Workspaces/Schemes" >>> Below it crashes (line is from your previous referred post on the >>> mailing list): >>> >>> scheme.mogene10stv1r4.na29 <- >>> import.exon.scheme("Scheme_MoGene10stv1r4_na29",filedir=scmdir, >>> paste(libdir,"MoGene-1_0-st-v1.r4.clf",sep="/"), >>> paste(libdir,"MoGene-1_0-st-v1.r4.pgf",sep="/"), >>> >>> >> paste(anndir,"MoGene- 1_0-st-v1.na29.mm9.probeset.fixed.csv",sep="/"), >> >> paste(anndir,"MoGene- 1_0-st-v1.na29.mm9.transcript.fixed.csv",sep="/") >> >>> ) >>> >>> Error message: >>> Rgui.exe - Application error. The instruction at "0x002288931" >>> references memory at "0x8d5056fc". The memory could not be "read". >>> >>> >>> >>>> sessionInfo() >>>> >>> R version 2.9.0 (2009-04-17) >>> i386-pc-mingw32 >>> >>> locale: >>> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United >>> Kingdom.1252;LC_MONETARY=English_United >>> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets >>> >> methods base >> >>> >>> other attached packages: >>> [1] xps_1.4.8 >>> >>> >>> >>> >>> >>> ------------------------------------------------ >>> Guido Hooiveld, PhD >>> Nutrition, Metabolism & Genomics Group Division of Human Nutrition >>> Wageningen University Biotechnion, Bomenweg 2 >>> NL-6703 HD Wageningen >>> the Netherlands >>> tel: (+)31 317 485788 >>> fax: (+)31 317 483342 >>> internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/> >>> email: guido.hooiveld at wur.nl >>> >>> >>> >> _______________________________________________ >> 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 >> >> >> > > > >
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Dear Christian, Thanks again for pointing me to the solution of my problem; it is now nicely outputting data for all probesets! I completely agree that including all probesets in the analysis is not wise to do (for reasons you mentioned), but since I am 'learning' XPS I noticed a discrepancy between the number of probes XPS produced data for (using it's default [script4xps.R] settings), and the number of probesets that were actually refered to on Affy's annotation file. And then I wanted to know how to calculate expression estimates for all probes (which was not clearly mentioned in ?rma)... Well, now I do know! :) Regards, Guido > -----Original Message----- > From: cstrato [mailto:cstrato at aon.at] > Sent: 18 August 2009 20:47 > To: Hooiveld, Guido > Cc: Bioconductor > Subject: Re: [BioC] FW: XPS crahses R session > > Dear Guido, > > Please have a look at the help file "?exonLevel". You will > see that setting exonlevel=c(992316,992316,992316) will > create expression levels for all 35518 (35519 - 1AFFX) probesets. > > However, I do not recommend this since I believe that adding > exon+intron+antigenomic probesets will only add noise to the results. > > Best regards > Christian > > Hooiveld, Guido wrote: > > Hi Christian, > > > > Indeed, downgrading to v5.22.00 of ROOT solved the problem I had (I > > initially had the impression the version of ROOT should _at > least_ be > > v5.22). XPS is now working fine. > > > > Still one question though, if I would like to calculate the > expression > > values of all 35519 probesets that are on the MoGene ST > array (as are > > e.g. visible in the Affy's NetAffx annotation file and the GEO > > platform entry @ NCBI > > > [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6246]), how to > > set the argument 'exonlevel'? > > If I set it @ 'all', then expression estimates of only > 28837 probesets > > are returned. With 'metacore+affx' this number is (reduced > to) 25690. > > > > Thanks, > > Guido > > > > > > > > > >> library(xps) > >> > > > > Welcome to xps version 1.4.8 > > an R wrapper for XPS - eXpression Profiling System > > (c) Copyright 2001-2009 by Christian Stratowa > > > > > >> libdir <- "d:/XPS/Affy/libraryfiles" > >> anndir <- "d:/XPS/Affy/Annotation" > >> scmdir <- "d:/XPS/CRAN/Workspaces/Schemes" > >> celdir <- "d:/XPS/ChipData/Gene/Linda" > >> datdir <- "d:/XPS/CRAN/Workspaces/ROOTData" > >> > > > > > >> scheme.mogene10stv1r4.na29 <- > >> > > import.exon.scheme("Scheme_MoGene10stv1r4_na29",filedir=scmdir, > > > > paste(libdir,"MoGene-1_0-st-v1.r4.clf",sep="/"), > > > > paste(libdir,"MoGene-1_0-st-v1.r4.pgf",sep="/"), > > > > > paste(anndir,"MoGene- 1_0-st-v1.na29.mm9.probeset.fixed.csv",sep="/"), > > > > > paste(anndir,"MoGene- 1_0-st-v1.na29.mm9.transcript.fixed.csv",sep="/") > > ) > > > >> scheme.MoGene <- > >> > > root.scheme(paste(scmdir,"Scheme_MoGene10stv1r4_na29.root",sep="/")) > > > >> data.linda <- root.data(scheme.MoGene, > >> > > paste(datdir,"MoGene_Linda_cel.root",sep="/")) > > > >> data.rma <- > >> > > > rma(data.linda,"MoGene_Linda_RMA",filedir=datdir,tmpdir="",background= > > "a > > ntigenomic",normalize=TRUE,exonlevel="metacore+affx",verbose=TRUE) > > > >> data.rma <- > >> > > > rma(data.linda,"MoGene_Linda_RMA2",filedir=datdir,tmpdir="",ba > ckground=" > > antigenomic",normalize=TRUE,exonlevel="all",verbose=TRUE) > > > > > > > > > > > >> -----Original Message----- > >> From: bioconductor-bounces at stat.math.ethz.ch > >> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf > Of cstrato > >> Sent: 17 August 2009 20:13 > >> To: Hooiveld, Guido; Bioconductor > >> Subject: Re: [BioC] FW: XPS crahses R session > >> > >> Dear Guido, > >> > >> Since Bioconductor has compiled the Windows version of xps > using root > >> 5.22.00 you need to install the binary of this version, as > mentioned > >> in "System Requirements". You can download this version from: > >> http://root.cern.ch/root/Version522.html > >> I would suggest to install version: root_v5.22.00.win32.vc90.msi > >> > >> Please see also my introductory comments for Windows users: > >> https://www.stat.math.ethz.ch/pipermail/bioconductor/2008-Dece > >> mber/025452.html > >> > >> > >> Please let me know if this solved your problem. > >> > >> Best regards > >> Christian > >> > >> P.S.: Although the BioC mailing list is currently down I > assume that > >> it will contain your question, thus I cc to the list. > >> > >> Hooiveld, Guido wrote: > >> > >>> > >>> Hi, > >>> Since the BioC mailing list seems not to work properly (i haven't > >>> received any BioC mails the last days), I am sending you > this email > >>> directly. > >>> > >>> Regards, > >>> Guido > >>> > >>> ------------------------------------------------ > >>> Guido Hooiveld, PhD > >>> Nutrition, Metabolism & Genomics Group Division of Human > Nutrition > >>> Wageningen University Biotechnion, Bomenweg 2 > >>> NL-6703 HD Wageningen > >>> the Netherlands > >>> tel: (+)31 317 485788 > >>> fax: (+)31 317 483342 > >>> internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/> > >>> email: guido.hooiveld at wur.nl > >>> > >>> > >>> > >>> > >>> > >> > --------------------------------------------------------------------- > >> - > >> > >>> -- > >>> *From:* Hooiveld, Guido > >>> *Sent:* 17 August 2009 17:50 > >>> *To:* bioconductor at stat.math.ethz.ch > >>> *Subject:* XPS crahses R session > >>> > >>> Dear Christian, > >>> > >>> I am new to XPS and i would like to use it to analyse > Mouse Gene ST > >>> arrays (MoGene ST arrays). However, XPS crashes my R session when > >>> trying to create a ROOT scheme file fore these arrays, > and i don't > >>> know what may go wrong. Hopefully you can advise. :) > >>> > >>> Thanks, > >>> Guido > >>> > >>> > >>> What did i do? > >>> - I am using a windows machine (WinXP-SP3, 4GB memory) > >>> - I installed ROOT v5.24.00 (1st) and XPS (2nd). PS: is > >>> > >> there a way to > >> > >>> check whether ROOT installed properly? > >>> - Then i downloaded the 'library' files', > >>> > >> MoGene-1_0-st-v1.r4.pgf and > >> > >>> MoGene-1_0-st-v1.r4.clf, and put them in a directory > >>> (D:\XPS\Affy\libraryfiles) > >>> - Next i downloaded the latest annotation files from Affymetrix > >>> (MoGene-1_0-st-v1.na29.mm9.transcript.csv and > >>> MoGene-1_0-st-v1.na29.mm9.probeset.csv), and repaired them > >>> > >> according > >> > >>> to your instructions here: > >>> > >>> > >> http://article.gmane.org/gmane.science.biology.informatics.con > >> ductor/24587. > >> > >>> The annotation files are in the dir D:\XPS\Affy\Annotation. > >>> - I also created a dir to save the ROOT scheme file > >>> (D:\XPS\CRAN\Workspaces\Schemes). > >>> > >>> When running XPS to create the scheme file R crashes... > >>> > >>> My lines of code: > >>> library(xps) > >>> libdir <- "d:/XPS/Affy/libraryfiles" > >>> anndir <- "d:/XPS/Affy/Annotation" > >>> scmdir <- "d:/XPS/CRAN/Workspaces/Schemes" > >>> Below it crashes (line is from your previous referred post on the > >>> mailing list): > >>> > >>> scheme.mogene10stv1r4.na29 <- > >>> import.exon.scheme("Scheme_MoGene10stv1r4_na29",filedir=scmdir, > >>> paste(libdir,"MoGene-1_0-st-v1.r4.clf",sep="/"), > >>> paste(libdir,"MoGene-1_0-st-v1.r4.pgf",sep="/"), > >>> > >>> > >> > paste(anndir,"MoGene- 1_0-st-v1.na29.mm9.probeset.fixed.csv",sep="/"), > >> > >> > paste(anndir,"MoGene- 1_0-st-v1.na29.mm9.transcript.fixed.csv",sep="/" > >> ) > >> > >>> ) > >>> > >>> Error message: > >>> Rgui.exe - Application error. The instruction at "0x002288931" > >>> references memory at "0x8d5056fc". The memory could not be "read". > >>> > >>> > >>> > >>>> sessionInfo() > >>>> > >>> R version 2.9.0 (2009-04-17) > >>> i386-pc-mingw32 > >>> > >>> locale: > >>> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > >>> Kingdom.1252;LC_MONETARY=English_United > >>> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > >>> > >>> attached base packages: > >>> [1] stats graphics grDevices utils datasets > >>> > >> methods base > >> > >>> > >>> other attached packages: > >>> [1] xps_1.4.8 > >>> > >>> > >>> > >>> > >>> > >>> ------------------------------------------------ > >>> Guido Hooiveld, PhD > >>> Nutrition, Metabolism & Genomics Group Division of Human > Nutrition > >>> Wageningen University Biotechnion, Bomenweg 2 > >>> NL-6703 HD Wageningen > >>> the Netherlands > >>> tel: (+)31 317 485788 > >>> fax: (+)31 317 483342 > >>> internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/> > >>> email: guido.hooiveld at wur.nl > >>> > >>> > >>> > >> _______________________________________________ > >> 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 > >> > >> > >> > > > > > > > > > > >
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