Hi
I have been trying to perform pathway analysis or overrepresentation analysis using KEGG pathway but unable to do so since I get an error that connection to API server failed.
Here’s the code and error from my R session:
mSet<-Setup.MapData(mSet, tmp.vec)
mSet<-CrossReferencing(mSet, “name”)
[1] “Loaded files from MetaboAnalyst web-server.”
[1] “Loaded files from MetaboAnalyst web-server.”
[1] “1”
[2] “Name matching OK, please inspect (and manual correct) the results then proceed.”
mSet<-CreateMappingResultTable(mSet)
[1] “Loaded files from MetaboAnalyst web-server.”
mSet<-GetCandidateList(mSet)
mSet<-SetKEGG.PathLib(mSet, “hsa”, “current”)
mSet<-SetMetabolomeFilter(mSet, F)
mSet<-CalculateOraScore(mSet, “rbc”, “hyperg”)
[1] “Loaded files from MetaboAnalyst web-server.”
[1] “Failed to connect to the API Server!”
[1] “Failed to perform pathway analysis!”
I want to note that ORA using smpdb_pathway worked to generate an enrichment plot. So this looks to be a KEGG pathway API issue from my understanding. Help please!