Failed to connect to the API Server

[MujeebQadiri]

Hi,

I have run the following commands (taken from the R command history from the web-tool)

mSet<-InitDataObjects("conc", "pathqea", FALSE)
mSet<-Read.TextData(mSet, "example_data.csv", "rowu", "disc");
mSet<-SanityCheckData(mSet)
mSet<-ReplaceMin(mSet);
mSet<-CrossReferencing(mSet, "name");
mSet<-CreateMappingResultTable(mSet)
mSet<-PreparePrenormData(mSet)
mSet<-Normalization(mSet, "NULL", "NULL", "NULL", ratio=FALSE, ratioNum=20)
mSet<-PlotNormSummary(mSet, "norm_1_", "png", 72, width=NA)
mSet<-PlotSampleNormSummary(mSet, "snorm_1_", "png", 72, width=NA)
mSet<-SetKEGG.PathLib(mSet, "dme", "current")
mSet<-SetMetabolomeFilter(mSet, F);
mSet<-CalculateQeaScore(mSet, "rbc", "gt")
mSet<-PlotPathSummary(mSet, F, "path_view_0_", "png", 72, width=NA, NA, NA )

I get the following error when running CalculateQeaScore(mSet, "rbc", "gt"):

> mSet<-CalculateQeaScore(mSet, "rbc", "gt")
[1] "Loaded files from MetaboAnalyst web-server."
[1] "Failed to connect to the API Server!"
[1] "Error! Pathway QEA via xialab.ca/api unsuccessful!"

Any help would be much appreciated.

[CrimsonUMO]

met the same problem and still don't know how can i do

[MujeebQadiri]

met the same problem and still don't know how can i do

Until they update/fix the API server, I have resorted to performing the analysis using their website. Not the fastest way to do it for multiple experiments but it works.

You may download the pathway analysis results and fine-tune the visualizations (in my case I wanted to change the axes and collect 8 different experiment results).

[mdidish]

For information, ORA using smpdb_pathway worked to generate an enrichment plot. Only KEGG pathway API is a problem.