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Old 03-21-2014, 01:18 PM   #51
bigmw
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Location: US

Join Date: Aug 2013
Posts: 123
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Well, you can check the first attached image in post 47. Obviously you do get different colors on pathview graphs. I think you might have checked the pathview output in the wrong directory:
kegg.dir = "~/RNAseq/13_Acute-Changes/13_GAGE_native_A1A2/A1A2pT2D/Pathview"

This is the directory storing original KEGG pathway graphs (and xml data). you should check in your current working directory for pathview output:
getwd()


Quote:
Originally Posted by sindrle View Post
Pasted wrong sessioninfo..

# > sessionInfo()
# R version 3.0.3 (2014-03-06)
# Platform: x86_64-apple-darwin10.8.0 (64-bit)
...

Pathview works, but I dont get colors or up/down regulated genes...
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