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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