To the developers,
I am trying to run a complete pathway analysis on oryza sativa japonica (osa) using the package GAGE and Pathview but I ran into problems as indicated in the title.
I am trying to run the codes as indicated on the tutorials as follows:
deseq2.fc=res.05_NILD_SWAD$log2FoldChange
names(deseq2.fc)=rownames(res.05_NILD_SWAD)
exp.fc=deseq2.fc
out.suffix="deseq2"
require(gage)
data("kegg.gs")
fc.kegg.p <- gage(exp.fc, gsets = kegg.gs, ref = NULL, samp = NULL)
sel <- fc.kegg.p$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 = "osa", out.suffix=out.suffix))
However, I ran into these series of warnings:
Info: Downloading xml files for osaNA, 1/1 pathways..
Warning: Download of osaNA xml file failed!
This pathway may not exist!
Info: Downloading png files for osaNA, 1/1 pathways..
Warning: Download of osaNA png file failed!
This pathway may not exist!
Warning: Failed to download KEGG xml/png files, osaNA skipped!
Info: Downloading xml files for osaNA, 1/1 pathways..
Warning: Download of osaNA xml file failed!
This pathway may not exist!
Info: Downloading png files for osaNA, 1/1 pathways..
Warning: Download of osaNA png file failed!
This pathway may not exist!
Warning: Failed to download KEGG xml/png files, osaNA skipped!
Info: Downloading xml files for osaNA, 1/1 pathways..
Warning: Download of osaNA xml file failed!
This pathway may not exist!
Info: Downloading png files for osaNA, 1/1 pathways..
Warning: Download of osaNA png file failed!
This pathway may not exist!
Warning: Failed to download KEGG xml/png files, osaNA skipped!
Warning messages:
1: In download.file(xml.url, xml.target, quiet = T) :
cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
2: In download.file(xml.url, xml.target, quiet = T) :
cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
3: In download.file(xml.url, xml.target, quiet = T) :
cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
Please advise.
Asher
