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CalculateGlobalTestScore(): $ operator is invalid for atomic vectors #305

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JG1ANDONLY opened this issue May 10, 2024 · 4 comments
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@JG1ANDONLY
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JG1ANDONLY commented May 10, 2024

This is my code to run metabolite enrichment analysis:
mSet<-InitDataObjects("conc", "msetqea", FALSE)
mSet<-Read.TextData(mSet, "placeholder.csv", "rowu", "disc")
mSet<-SanityCheckData(mSet)
mSet<-ReplaceMin(mSet)
mSet<-CrossReferencing(mSet, "name")
mSet<-CreateMappingResultTable(mSet)
mSet<-PreparePrenormData(mSet)
mSet<-Normalization(mSet, "NULL", "LogNorm", "NULL", ratio=FALSE, ratioNum=20)
mSet<-PlotNormSummary(mSet, "norm_0_", "png", 72, width=NA)
mSet<-PlotSampleNormSummary(mSet, "snorm_0_", "png", 72, width=NA)
mSet<-SetMetabolomeFilter(mSet, F)
mSet<-SetCurrentMsetLib(mSet, "kegg_pathway", 2)
mSet<-CalculateGlobalTestScore(mSet)

The error is here: mSet<-CalculateGlobalTestScore(mSet)
and the error messages are:
[1] "Failed to connect to the API Server!"
[1] "Error! QEA Pathway Analysis via xialab.ca/api unsuccessful!"
Error in mSetObj$analSet : $ operator is invalid for atomic vectors

How do I solve this problem? This issue appeared only when I wanted to use KEGG. When I was playing with SMPDB ('smpdb_pathway'), there is no error generated.

@JG1ANDONLY
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Could anyone provide feedback on whether the KEGG database might have been out of service while using R? Your assistance is greatly appreciated!

@kazehaya-Nini
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I encountered the same problem. This issue has been going on for half a month

@JG1ANDONLY
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I encountered the same problem. This issue has been going on for half a month

Can you try SMPDB? For me, SMPDB works, but KEGG does not.

@kazehaya-Nini
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I tried it and had the same result as you

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