Question: GAGE for pathway analysis. How to visualize down-regulated pathways?
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gravatar for Parham
4.7 years ago by
Parham1.4k
Sweden
Parham1.4k wrote:

Hi, I am following this workflow. At step 6.1 second paragraph it says here we only visualize up-regulated pathways! I wonder how should I change the codes to visualize the down-regulated pathways? A beginner is writing this!  

A second question I have is, in last paragraph of same part (6.1) it says we can use Pathview to visualize RNA-Seq data (exp.fc) on all interesting pathways! I wonder is it something else than what I got from the output of

 > pv.out.lits <- sapply(path.ids2, function(pid) pathview(gene.data=exp.fc,

+ pathway.id=pid, species="spo", out.suffix=out.suffix, gene.idtype="KEGG")) 

gage down-regulated pathway • 1.7k views
ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by Parham1.4k
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