[BioC] An importMAGEML problem in RMAGEML Package

[Wolfgang Huber]

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
> 
> _______________________________________________
> 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