[BioC] mageml

[Vincent Carey 525-2265]

> 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 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                                 //=\
>
>
>