[BioC] mageml

[Cary Miller]

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 at 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                                 //=\