Question: Kegg analysis for s.pombe
1
gravatar for Parham
4.8 years ago by
Parham1.4k
Sweden
Parham1.4k wrote:

Hi, I am trying this workflow. I am wondering for pathway analysis in part 6.1 DESeq2, how should I change it to make the kegg data suitable for s.pombe. The scripts are for human as they are. The codes follow as:

require(gage)
datakegg.gs)
fc.kegg.p <- gage(exp.fc, gsets = kegg.gs, ref = NULL, samp = NULL)
sel <- fc.kegg.p$greater[, "q.val"] < 0.1 &
!is.na(fc.kegg.p$greater[, "q.val"])
path.ids <- rownames(fc.kegg.p$greater)[sel]
sel.l <- fc.kegg.p$less[, "q.val"] < 0.1 &
!is.na(fc.kegg.p$less[,"q.val"])
path.ids.l <- rownames(fc.kegg.p$less)[sel.l]
path.ids2 <- substr(c(path.ids, path.ids.l), 1, 8)
require(pathview)
#view first 3 pathways as demo
pv.out.list <- sapply(path.ids2[1:3], function(pid) pathview(
gene.data = exp.fc, pathway.id = pid,
species = "hsa", out.suffix=out.suffix))

Please help me with this!

 

kegg s. pombe • 1.5k views
ADD COMMENTlink modified 4.8 years ago by Neilfws48k • written 4.8 years ago by Parham1.4k

One good idea would be to ask the author of the original work. Another, would be to break down your problem into smaller pieces, and to ask people here, one step at a time. I am not sure that someone would invest time and effort to debug the _whole_ thing for you. Sorry.

ADD REPLYlink written 4.8 years ago by Pavel Senin1.9k

It's not actually as complex as it looks; see my answer.

ADD REPLYlink written 4.8 years ago by Neilfws48k
1
gravatar for Neilfws
4.8 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

KEGG uses 3 or 4 letter codes for organisms. So all you need to do is change "hsa" (Homo sapiens) to "spo" ("Schizosaccharomyces pombe").

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by Neilfws48k

Nice! In fact, respect for solving the problem! Note however, that the 4 letter codes exist as well, i can see more than 250 of these. 

ADD REPLYlink written 4.8 years ago by Pavel Senin1.9k

correct and edited accordingly

ADD REPLYlink written 4.8 years ago by Neilfws48k

Just that?! In that case I tried it and still I am getting the same error! I have a same thread going on, on seqanswers you can see it here. Even I was advised differently the outcome is the same error yet! Do you have any other advise?

ADD REPLYlink written 4.8 years ago by Parham1.4k
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