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Old 03-12-2014, 05:36 PM   #23
bigmw
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Location: US

Join Date: Aug 2013
Posts: 123
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This is indeed a typo, it should be cuff.fc instead of exp.fc at this step. And you will assign cuff.fc to exp.fc in a later step, and then work exclusively on exp.fc:
range(cuff.fc)
#remove the -Inf and Inf values, which block the downstream analysis
cuff.fc[cuff.fc>10]=10
cuff.fc[cuff.fc< -10]=-10
exp.fc=cuff.fc
out.suffix="cuff"


BTW, the demo example uses human data, and you have to specify organism to be Sus scrofa (pig) for your data when you map gene sybmols to entrez gene IDs as below:
gnames.eg=pathview::id2eg(gnames, category ="symbol", org=="Ss")

Last edited by bigmw; 03-13-2014 at 12:40 PM.
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