[BioC] RMAGEML and JVM

[Wolfgang Huber]

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 at 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
>