[R] Pathview xml issue

Yin dawn1313 at gmail.com
Tue Nov 7 20:15:51 CET 2017


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 =
  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!

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