[BioC] An importMAGEML problem in RMAGEML Package
Wolfgang Huber
huber at ebi.ac.uk
Tue Aug 5 12:48:43 CEST 2008
Dear Haonan,
where did you get that file E-TABM-421.mageml.tar.gz from?
Neither ArrayExpress (http://www.ebi.ac.uk/microarray-as/ae)
nor Google appear to know anything about it.
Best wishes
Wolfgang
------------------------------------------------------------------
Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
05/08/2008 10:19 Haonan WU scripsit
> Hello,
>
> I am trying to use the RMAGEML package to read in MAGE-ML files which I
> had downloaded from the EBI ArrayExpress database. However, when I try and
> use the importMAGEML()
> function, I get this error:
> --------------------------------------------
> - Java Virtual Machine is running -
> parsing MAGEML files
>
> *** caught segfault ***
> address (nil), cause 'memory not mapped'
>
> Traceback:
> 1: .Call("getVoidArrayStr", "getBioSequenceID", mageOM,
> ..rmagemlJVM at jvmptr, PACKAGE = "RMAGEML")
> 2: getGnames(mageOM, arrayID = arrayID, DED = DED, db = db, package =
> package)
> 3: importMAGEML(directory = "/home/hwu/E-TABM-421/E-TABM-421_download",
> package = "marray", arrayID = "A-MEXP-931", DED = "none", QTD =
> "none", name.Rf = "QT:F635 Mean", name.Rb = "QT:B635 Median", name.Gf
> = "QT:F532 Mean", name.Gb = "QT:B532 Median")
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
> -------------------------------------------------------
>
> Here are some descriptions on the structure of my data, it is a
> MEGAML(.gz): E-TABM-421.mageml.tar.gz, and I un-ziped it at my local
> directory in the folder:E-TABM-421_download, and imported it by its full
> directory.(there are there files in it respectively:
> E-TABM-421.xml,nrmzd_Sample_Probe_Profile.txt.proc, and
> Sample_Probe_Profile.txt.proc.)
>
> And the R cmd I used:
> ----------------------------------------------------
>> library(RMAGEML)
> Loading required package: marray
> Loading required package: limma
> Loading required package: Biobase
> Loading required package: tools
>
> Welcome to Bioconductor
>
> Vignettes contain introductory material. To view, type
> 'openVignette()'. To cite Bioconductor, see
> 'citation("Biobase")' and for packages 'citation(pkgname)'.
>
>> raw <- importMAGEML(directory =
> "/home/hwu/E-TABM-421/E-TABM-421_download", package = "marray",arrayID =
> "A-MEXP-931", DED = "none", QTD = "none", name.Rf = "QT:F635
> Mean",name.Rb = "QT:B635 Median", name.Gf = "QT:F532 Mean",name.Gb =
> "QT:B532 Median")
> ---------------------------------------------------------------
>
> I am looking forward to your help and advices, Thanks in advance!
>
> Haonan WU
>
> Research Assistant, Department of Bioinformatics, Fraunhofer Institute for
> Algorithms and Scientific Computing (SCAI),
> Mobile: (+49) (0)163-2379046
> E-mail:
> wuh at cs.uni-bonn.com
> haonan.wu at scai.fraunhofer.de
>
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