Question: An importMAGEML problem in RMAGEML Package
0
gravatar for Haonan WU
11.3 years ago by
Haonan WU10
Haonan WU10 wrote:
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
rmageml arrayexpress • 442 views
ADD COMMENTlink modified 11.3 years ago by Wolfgang Huber13k • written 11.3 years ago by Haonan WU10
Answer: An importMAGEML problem in RMAGEML Package
0
gravatar for Wolfgang Huber
11.3 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
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
ADD COMMENTlink written 11.3 years ago by Wolfgang Huber13k
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