[BioC] MAGE_ML and RMAGEML

[Martin Morgan]

Hi Eugene,

I don't know of an easy answer. A difficult answer might be the XML
package, with things like

> library(XML)
> ## This is from ArrayExpresss
> fl <- file.path("/loc/mtmorgan/tmp/E-MEXP-140",
+   "Auxin_induced_effects_investigated_using_bead-purified_probe_arrays_1_qtd.xml")
> res <- xmlTreeParse(fl,useInternalNode=TRUE)
> 
> ## How many reporters?
> reporters <- getNodeSet(res, "//Reporter_ref")
> length(reporters)
[1] 19328
> ## each reporter includes an encoded identifier
> head(sapply(reporters, xmlGetAttr, "identifier"))
[1] "R:A-MEXP-68:96103_2"  "R:A-MEXP-68:96103_4"  "R:A-MEXP-68:96103_6" 
[4] "R:A-MEXP-68:96103_8"  "R:A-MEXP-68:96103_26" "R:A-MEXP-68:96103_28"
> 
> ## 'MeasuredBioAssayData stores cel-file level data; in AE these are
> ## usually stored as DataExternal, i.e., tab- or
> ## whitespace-delimited files.
mbad <- getNodeSet(res, "//MeasuredBioAssayData")
> sapply(sapply(mbad, getNodeSet, "//DataExternal"),
+        xmlGetAttr, "filenameURI")
[1] "Untreated-vs-30min.txt"     "30min-vs-Untreated.txt"    
[3] "Untreated-vs-120min.txt"    "120min-vs-Untreated.txt"   
[5] "Untreated-vs-240min.txt"    "240min-vs-Untreated.txt"   
[7] "Untreated-vs-Untreated.txt"

to extract relevant information from the XML. This is likely to end up
requiring detailed knowledge of MAGE-ML and of Bioconductor data
structures.

Martin

"Eugene Bolotin" <ybolo001 at student.ucr.edu> writes:

> Dear Developers,
> I am having trouble getting bioconductor to read MAGE-ML files.
> My operating system is OSX, and I can not install SJava that RMAGEML
> requires.
> Has anyone gotten RMAGEML working for OSX, or knows any other ways to cram
> MAGE-ML format into limma.
> If so, how?
> Thanks a lot.
>
> -- 
> Eugene Bolotin
> Ph.D. candidate
> Genetics Genomics and Bioinformatics
> University of California Riverside
> ybolo001 at student.ucr.edu
> Dr. Frances Sladek Lab
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org