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I am trying to run MetaboAnalyst 3.0.3 Pathway Analysis on R (see session information below), and I am getting an error when I try to run the second line of code.

Pathway Analysis Tutorial

I keep getting this error:

> mSet<-InitDataObjects(data.type = "conc", anal.type = "pathora", FALSE)
Error: $ operator is invalid for atomic vectors

Session Info

I tried following this advice but will no luck. I would really appreciate guidance on this seemingly trivial problem!

mikamatvat
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  • Have you tried updating each of the packages required in MetaboAnalystR? : `pacman::p_load("impute", "pcaMethods", "globaltest", "GlobalAncova", "Rgraphviz", "preprocessCore", "genefilter", "SSPA", "sva", "limma", "KEGGgraph", "siggenes","BiocParallel", "MSnbase", "multtest","RBGL","edgeR","fgsea","httr","qs")` – Basti Jul 01 '21 at 10:24
  • Thank you for the suggestion! I did try that and unfortunately I get the same error. I am not sure if the dependencies that I have loaded are messing with MetaboAnalyst. Any other insights would be appreciated, thank you! – mikamatvat Jul 01 '21 at 11:15
  • Maybe you can have a look at this, it seems the same problem of you occurs, maybe related to a problem with a package ! : https://github.com/xia-lab/MetaboAnalystR/issues/16 – Basti Jul 01 '21 at 11:38

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