[BioC] FW: XPS crahses R session
Hooiveld, Guido
Guido.Hooiveld at wur.nl
Tue Aug 18 21:51:16 CEST 2009
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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