Hi Wolfgang,

thank you for your reply! I saw this paper but as far as I understood, the
new tab format is not yet in use or am I wrong? Of course, then it would be
a lot better to use the new format...

Regards
Michaela


2007/7/10, Wolfgang Huber <huber@ebi.ac.uk>:
>
> Dear Michaela,
>
> this does not directly answer your question... but rather than
> flagellating yourself with MAGE-ML you might want to have a look at the
> recent proposal from MGED for a simpler data format:
>
> A simple spreadsheet-based, MIAME-supportive format for microarray data:
> MAGE-TAB.
> Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E,
> Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J,
> Sherlock G, Stoeckert CJ, White J, Whetzel PL, Wymore F, Parkinson H,
> Sarkans U, Ball CA, Brazma A.
> BMC Bioinformatics. 2006 Nov 6;7:489.
> http://www.biomedcentral.com/1471-2105/7/489
>
> Best wishes
> Wolfgang
>
> ------------------------------------------------------------------
> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
>
>
>
> Michaela Gündel ha scritto:
> > Dear list,
> >
> > creating a microarray workflow for my Master Thesis, I am facing a
> > problem concerning the RMAGEML package.
> >
> > I am constructing the workflow from Java using the BioC packages. I set
> > up an Rengine in Java and from this, I call R commands using
> > Rengine.eval(). The problem I am facing now is that I want to read in
> > MIAME compliant data with the RMAGEML package, which, from R directly,
> > works perfectly. However, the problem is that the package creates a JVM
> > which of course does not work calling it from an already existing JVM.
> >
> > Is there any way of
> > - either using the existing JVM in the importMAGEOM function (there:
> > mageOM <- .Call("newRMAGESTK", directory, ..rmagemlJVM@jvmptr, PACKAGE =
> > "RMAGEML") )
> > - or reading the MAGEML document using MAGE-STK and converting the input
> > from the then Java object to an R object that I can read into R (I am
> > working with RGLists mainly)?
> >
> > Your help is very much appreciated!
> >
> > I am using:
> >> sessionInfo()
> > R version 2.5.0 (2007-04-23)
> > i686-pc-linux-gnu
> >
> > locale:
> >
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] "tcltk" "splines" "tools" "stats" "graphics" "grDevices"
> > [7] "utils" "datasets" "methods" "base"
> >
> > other attached packages:
> > convert RMAGEML marray tkWidgets DynDoc widgetTools
> > "1.10.0" "2.10.0" "1.14.0" "1.14.0" "1.14.0" "1.12.0"
> > genefilter survival limma goCluster Biobase
> > "1.14.1" "2.31" "2.10.5" "1.4.0" "1.14.0"
> >
> > Thanks a lot in advance,
> >
> > Michaela
> >
>

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