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Question: mageml
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gravatar for Cary Miller
14.0 years ago by
Cary Miller20
Cary Miller20 wrote:
Hi all, I am attempting to use public MAGEML data without success. My current datasets are E-CAGE-{2,3,4} from ArrayExpress. According to the tutorial a MAGEML file requires packages BioAssayData BioAssay BioMaterial BioSequence ArrayDesign DesignElement I suppose this is the problem because inspection of package content shows this: > magePackageDetector(ecage3) File aVIB-Col_vs_aUNIL-Col.xml contains the following packages: BioMaterial_package BioAssay_package QuantitationType_package BioAssayData_package There is only 1 xml file included with the data. How can I get the correct packages? Any help will be appreciated. Thanks --cam -- //=\ Cary Miller //=\ \=// Center for Computational Pharmacology \=// //=\ University of Colorado Health Sciences Center //=\ \=// http://compbio.uchsc.edu/Hunter_lab/Miller \=// //=\ (303) 315-1584 //=\
ADD COMMENTlink modified 14.0 years ago by Vincent J. Carey, Jr.6.2k • written 14.0 years ago by Cary Miller20
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gravatar for Vincent J. Carey, Jr.
14.0 years ago by
United States
Vincent J. Carey, Jr.6.2k wrote:
> Hi all, > I am attempting to use public MAGEML data without success. My current > datasets are E-CAGE-{2,3,4} from ArrayExpress. According to the tutorial > a MAGEML file requires packages > BioAssayData > BioAssay > BioMaterial > BioSequence > ArrayDesign > DesignElement please say more about what "without success" means. what are the specific error messages you are obtaining? > > I suppose this is the problem because inspection of package content shows > this: > > magePackageDetector(ecage3) > > File aVIB-Col_vs_aUNIL-Col.xml contains the following packages: > > BioMaterial_package > BioAssay_package > QuantitationType_package > BioAssayData_package > > There is only 1 xml file included with the data. How can I get the > correct packages? Any help will be appreciated. Thanks > --cam > > -- > //=\ Cary Miller //=\ > \=// Center for Computational Pharmacology \=// > //=\ University of Colorado Health Sciences Center //=\ > \=// http://compbio.uchsc.edu/Hunter_lab/Miller \=// > //=\ (303) 315-1584 //=\ > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
ADD COMMENTlink written 14.0 years ago by Vincent J. Carey, Jr.6.2k
Here is more diagnostic information. It's not very informative. I will try to break it in other ways and see if more revealing error messages appear. > dir(datadir) [1] "aVIB-Col_vs_aVIB-Col.xml" "Cat175_Merged_3_5_cr.txt" [3] "E-CAGE-2.tar" "Merged3-5+c-r.txt" > xfile="aVIB-Col_vs_aVIB-Col.xml" > design = readMageDesign(file=xfile, datadir=datadir) Parsing XML documents ... (can take several minutes) Error in readMageDesign(file = xfile, datadir = datadir) : This dataset can not be imported into BioConductor > On Tue, 4 Nov 2003, Vincent Carey 525-2265 wrote: > > > Hi all, > > I am attempting to use public MAGEML data without success. My current > > datasets are E-CAGE-{2,3,4} from ArrayExpress. According to the tutorial > > a MAGEML file requires packages > > BioAssayData > > BioAssay > > BioMaterial > > BioSequence > > ArrayDesign > > DesignElement > > please say more about what "without success" means. what > are the specific error messages you are obtaining? > > > > > I suppose this is the problem because inspection of package content shows > > this: > > > magePackageDetector(ecage3) > > > > File aVIB-Col_vs_aUNIL-Col.xml contains the following packages: > > > > BioMaterial_package > > BioAssay_package > > QuantitationType_package > > BioAssayData_package > > > > There is only 1 xml file included with the data. How can I get the > > correct packages? Any help will be appreciated. Thanks > > --cam > > > > -- > > //=\ Cary Miller //=\ > > \=// Center for Computational Pharmacology \=// > > //=\ University of Colorado Health Sciences Center //=\ > > \=// http://compbio.uchsc.edu/Hunter_lab/Miller \=// > > //=\ (303) 315-1584 //=\ > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > -- //=\ Cary Miller //=\ \=// Center for Computational Pharmacology \=// //=\ University of Colorado Health Sciences Center //=\ \=// http://compbio.uchsc.edu/Hunter_lab/Miller \=// //=\ (303) 315-1584 //=\
ADD REPLYlink written 14.0 years ago by Cary Miller20
> Here is more diagnostic information. It's not very informative. I will I agree. This is something the MAGEML developers need to look at. This also exposes the role for document validation via a DTD or a schema. You may be able to get more information by running options(error=recover) before you try the readMage call, to find out which R function is throwing the error. As you noted, there appears to be a requirement that a certain minimal set of MAGEML packages be required represented in your document. You may be able to "fake" the representation by adding empty nodes corresponding to the ones that are missing, and get the read function to complete without error. But if MAGEML actually needs the data in the missing packages to deal with the packages that you do have, this will not help much. The real problem is to define and verify MAGEML compliance of any given file that will be processed by the package. The DTD should be used for performing such verification. Furthermore, the R package should probably by default reject any input that is not a valid MAGEML document. > try to break it in other ways and see if more revealing error messages > appear. > > > dir(datadir) > [1] "aVIB-Col_vs_aVIB-Col.xml" "Cat175_Merged_3_5_cr.txt" > [3] "E-CAGE-2.tar" "Merged3-5+c-r.txt" > > xfile="aVIB-Col_vs_aVIB-Col.xml" > > design = readMageDesign(file=xfile, datadir=datadir) > Parsing XML documents ... (can take several minutes) > Error in readMageDesign(file = xfile, datadir = datadir) : > This dataset can not be imported into BioConductor > > > > > On Tue, 4 Nov 2003, Vincent Carey 525-2265 wrote: > > > > > > Hi all, > > > I am attempting to use public MAGEML data without success. My current > > > datasets are E-CAGE-{2,3,4} from ArrayExpress. According to the tutorial > > > a MAGEML file requires packages > > > BioAssayData > > > BioAssay > > > BioMaterial > > > BioSequence > > > ArrayDesign > > > DesignElement > > > > please say more about what "without success" means. what > > are the specific error messages you are obtaining? > > > > > > > > I suppose this is the problem because inspection of package content shows > > > this: > > > > magePackageDetector(ecage3) > > > > > > File aVIB-Col_vs_aUNIL-Col.xml contains the following packages: > > > > > > BioMaterial_package > > > BioAssay_package > > > QuantitationType_package > > > BioAssayData_package > > > > > > There is only 1 xml file included with the data. How can I get the > > > correct packages? Any help will be appreciated. Thanks > > > --cam > > > > > > -- > > > //=\ Cary Miller //=\ > > > \=// Center for Computational Pharmacology \=// > > > //=\ University of Colorado Health Sciences Center //=\ > > > \=// http://compbio.uchsc.edu/Hunter_lab/Miller \=// > > > //=\ (303) 315-1584 //=\ > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > > -- > //=\ Cary Miller //=\ > \=// Center for Computational Pharmacology \=// > //=\ University of Colorado Health Sciences Center //=\ > \=// http://compbio.uchsc.edu/Hunter_lab/Miller \=// > //=\ (303) 315-1584 //=\ > > >
ADD REPLYlink written 14.0 years ago by Vincent J. Carey, Jr.6.2k
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