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Old 02-21-2014, 09:17 AM   #18
shriram
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Location: UK

Join Date: May 2010
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Quote:
Originally Posted by shriram View Post
Hi
I am using pathview for yeast however I get following error while retrieving pathway information for 19 different pathways.
[1] "Downloading xml files for sce04113 Meiosis - yeast, 1/19 pathways.."
[1] "Downloading png files for sce04113 Meiosis - yeast, 1/19 pathways.."
Download of sce04113 Meiosis - yeast xml and png files failed!
Failed to download KEGG xml/png files, sce04113 Meiosis - yeast skipped!

Same functionality works fine with human data.

below is my R version
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

Thanks
Shriram
############
Issue resolved
by taking substring of actual pathway name in kegg and specifying gene.idtype="KEGG"
path.ids <- substr(path.ids, 1, 8)
############
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