[BioC] FW: XPS crahses R session
cstrato
cstrato at aon.at
Tue Aug 18 20:47:10 CEST 2009
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="",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
>>>
>>>
>>>
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>
>
>
>
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