Hi!
Here is my code, my input is from DESeq2 results.
deseq2.fc=timepointsResults$log2FoldChange;
names(deseq2.fc)=rownames(timepointsResults);
exp.fc=deseq2.fc;
out.suffix="timepointsResultsDESeq2"
require(gage);
data(kegg.gs);
dir.create("/Volumes/timemachine/HTseq_DEseq2/1_Results/GAGE_upregulated_timepointsResults");
setwd("/Volumes/timemachine/HTseq_DEseq2/1_Results/GAGE_upregulated_timepointsResults");
fc.kegg.p <- gage(exp.fc, gsets = kegg.gs, ref = NULL, samp = NULL, same.dir = TRUE) ;
sel <- fc.kegg.p$greater[, "q.val"] > 0.1 & !is.na(fc.kegg.p$greater[, "q.val"]) ;
path.ids <- rownames(fc.kegg.p$greater)[sel] ;
path.ids2 <- substr(path.ids, 1, 8) ;
require(pathview) ;
pv.out.list <- sapply(path.ids2[1:3], function(pid) pathview(gene.data = exp.fc, pathway.id = pid, species = "hsa", out.suffix=out.suffix))
I just want to look for the top 3 upregulated pathways, but I only get an "404 not found" error.
Anyone understand this?
Here is my code, my input is from DESeq2 results.
deseq2.fc=timepointsResults$log2FoldChange;
names(deseq2.fc)=rownames(timepointsResults);
exp.fc=deseq2.fc;
out.suffix="timepointsResultsDESeq2"
require(gage);
data(kegg.gs);
dir.create("/Volumes/timemachine/HTseq_DEseq2/1_Results/GAGE_upregulated_timepointsResults");
setwd("/Volumes/timemachine/HTseq_DEseq2/1_Results/GAGE_upregulated_timepointsResults");
fc.kegg.p <- gage(exp.fc, gsets = kegg.gs, ref = NULL, samp = NULL, same.dir = TRUE) ;
sel <- fc.kegg.p$greater[, "q.val"] > 0.1 & !is.na(fc.kegg.p$greater[, "q.val"]) ;
path.ids <- rownames(fc.kegg.p$greater)[sel] ;
path.ids2 <- substr(path.ids, 1, 8) ;
require(pathview) ;
pv.out.list <- sapply(path.ids2[1:3], function(pid) pathview(gene.data = exp.fc, pathway.id = pid, species = "hsa", out.suffix=out.suffix))
I just want to look for the top 3 upregulated pathways, but I only get an "404 not found" error.
Anyone understand this?
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