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 > >> > >> > >> > > > > > > > > > > >