[R] Pathview xml issue

[Jeff Newmiller]

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 <dawn1313 at 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]]
>
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