Between the lack of a reproducible example and the question being about a Bioconductor package, you probably won't see much response here. Try the Bioconductor mailing list? -- Sent from my phone. Please excuse my brevity.
On November 7, 2017 11:15:51 AM PST, Yin <dawn1...@gmail.com> wrote: >Hi, > >I'm using GAGE/pathview to analyze my RNA-seq and phospho-protein data. >The >following error occurs after this command line below: > >>pv.out.list <- sapply(path.ids2[1:3], function(pid) pathview( >gene.data = cnts.d, pathway.id = pid, gene.idtype="SYMBOL",kegg.native >= >F, >same.layer = T, species = "hsa", kegg.dir = "test", out.suffix = "up")) > > >Start tag expected, '<' not found >Warning: Parsing test/hsa04510.xml file failed, please check the file! > >That .xml file is empty, while .png file exists. The issue is there is >no >pathway with my data mapped (red and blue nodes). Can you please help >that? > >Thank you! >Best, >Shu > > [[alternative HTML version deleted]] > >______________________________________________ >R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide >http://www.R-project.org/posting-guide.html >and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
