I have 2 groups, sick and healthy calves. I tried to do quantitative enrichment analysis with metabolite concentrations.
However, in my final output for the Network View, although the “?” icon indicates you can double click on a node to find the associated metabolites, this feature is not working. Furthermore, when I check the enrichment table at the bottom of the output, if I try to view details in order to look for box plots of sick vs healthy I see nothing…
If I use the example dataset with cachexia and normal samples, I still get no metabolite sets if I try and double click the nodes from the network view. But I will get box plots of cachexia vs normal samples when I view the details option from the metabolite set data.
This is the R output from trying to run the calf metabolite data
| 1. | mSet<-InitDataObjects(conc, msetqea, FALSE) |
|---|---|
| 2. | mSet<-Read.TextData(mSet, drenaud_msteele_calflong_metametab.csv, rowu, disc); |
| 3. | mSet<-SanityCheckData(mSet) |
| 4. | mSet<-ReplaceMin(mSet); |
| 5. | mSet<-CrossReferencing(mSet, name); |
| 6. | mSet<-CreateMappingResultTable(mSet) |
| 7. | mSet<-PreparePrenormData(mSet) |
| 8. | mSet<-Normalization(mSet, MedianNorm, LogNorm, ParetoNorm, ratio=FALSE, ratioNum=20) |
| 9. | mSet<-PlotNormSummary(mSet, norm_0_, png, 72, width=NA) |
| 10. | mSet<-PlotSampleNormSummary(mSet, snorm_0_, png, 72, width=NA) |
| 11. | mSet<-SetMetabolomeFilter(mSet, F); |
| 12. | mSet<-SetCurrentMsetLib(mSet, fecal, 2); |
| 13. | mSet<-CalculateGlobalTestScore(mSet) |
| 14. | mSet<-.prepare.globaltest.score(mSet) |
| 15. | dat.in ← qs::qread(dat.in.qs);dat.in$my.res ← dat.in$my.fun();qs::qsave(dat.in, file=dat.in.qs); |
| 16. | mSet<-.save.globaltest.score(mSet) |
| 17. | mSet<-PlotQEA.Overview(mSet, qea_0_, net, png, 72, width=NA) |
| 18. | mSet<-PlotEnrichDotPlot(mSet, qea, qea_dot_0_, png, 72, width=NA) |