Question: MAGE-ML reading
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gravatar for Vincent J. Carey, Jr.
14.6 years ago by
United States
Vincent J. Carey, Jr.6.3k wrote:
> I would like to read MAGE-ML, but I have not been able to get SJava to > install on MacOS. Are there other options to read MAGE-ML besides > RMAGEML (which requires SJava)? There is a version of SJava that ports to Mac OSX. It is made available by Simon Urbanek http://stats.math.uni-augsburg.de/~urbanek/SJava_0.65-X.tar.gz I have not tried it with R 2.0.1. This version of SJava lacks some important features of SJava_0.67-3 which is known to work with RMAGEML. You may have to modify the RMAGEML source a bit to get it to install with this old version of SJava -- you may have to relax the SJava version dependency. And this may lead to problems. But I think it is worth a try. You could parse and process the MAGE-ML using the XML package. If you had a clear and fairly restricted set of elements that you needed to grab, this might be very effective. The nice thing about RMAGEML is that it can in principle reflect anything in the MAGE-OM as captured by the java MAGEstk. RMAGEML has the resources to translate elements of MAGE-OM directly into elements of marray class instances. There is also a perl MAGEstk, I believe. One might get an interface through RSPerl. Please keep us informed of successes and failures in using MAGEML documents with Bioconductor. > > Thanks, > Sean > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
rmageml process marray sjava • 465 views
ADD COMMENTlink modified 14.6 years ago by Sean Davis21k • written 14.6 years ago by Vincent J. Carey, Jr.6.3k
Answer: MAGE-ML reading
0
gravatar for Sean Davis
14.6 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Apr 1, 2005, at 3:34 PM, Vincent Carey 525-2265 wrote: > >> I would like to read MAGE-ML, but I have not been able to get SJava to >> install on MacOS. Are there other options to read MAGE-ML besides >> RMAGEML (which requires SJava)? > > There is a version of SJava that ports to Mac OSX. It is made > available by Simon Urbanek > > http://stats.math.uni-augsburg.de/~urbanek/SJava_0.65-X.tar.gz > > I have not tried it with R 2.0.1. This version of SJava > lacks some important features of SJava_0.67-3 which is known > to work with RMAGEML. You may have to modify the RMAGEML > source a bit to get it to install with this old version of > SJava -- you may have to relax the SJava version dependency. > And this may lead to problems. But I think it is worth a > try. > > You could parse and process the MAGE-ML using the XML package. > If you had a clear and fairly restricted set of elements that you > needed to grab, this might be very effective. > > The nice thing about RMAGEML is that it can in principle > reflect anything in the MAGE-OM as captured by the java MAGEstk. > RMAGEML has the resources to translate elements of MAGE-OM directly > into elements of marray class instances. > > There is also a perl MAGEstk, I believe. One might get an > interface through RSPerl. > > Please keep us informed of successes and failures in using > MAGEML documents with Bioconductor. > Thanks, Vince. Just so you know why I ask, one of our new array platforms dumps straight MAGE-ML, so I am excited to have those data available. As for RSPerl, I haven't had much luck (although I haven't tried with 2.0.1) with installing it, either. I'll need to give it a try again, as I do use perl quite a bit. Sean
ADD COMMENTlink written 14.6 years ago by Sean Davis21k
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