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Old 05-16-2017, 06:48 PM   #2
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Location: US

Join Date: Aug 2013
Posts: 123

gage does use the latest data from KEGG if you generate gene set data using kegg.gsets() function. However, the reference pathway list could be out of date. The reason you see NA for 80 pathways is that those pathways are out of the set.size range. In other words, they may have too few genes mapped, hence no gene set test were done on them.
The greater and less elements in the result list correspond to up and down regulation test on all pathways (gene sets), not just the significant ones. You want to go though the gage function documentation for details, something like:
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