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Old 03-15-2014, 06:08 PM   #30
bigmw
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Location: US

Join Date: Aug 2013
Posts: 123
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R does not remember the old kegg.gs, if you assign the name to a new gene set data. If you are sure your code was right, then very likely your data had some problem. To locate the problem, you can restart a new R session and run the same analysis code on your problematic data till the pathview step. If you still get the same error message, run the following code, and post your output here so that we can check what happened to your data:

str(cuff.fc)
head(cuff.fc)
lapply(kegg.gs[1:3], head, 3)
head(fc.kegg.p$greater)
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