The issue about running the function PerformPSEA ()

MetaboAnalyst
,
1

Hi dear developers,
I followed the tutorial to run the scripts one by one using the example data, did not change anything,
However, I got the following error information:

mSet<-PerformPSEA(mSet, “hsa_mfn”, “current”, minLib = 3,permNum =100)
[1] “Got 2499 mass features.”
[1] “1616 inital ECs created!”
Error in UseMethod(“melt”, data) :
no applicable method for ‘melt’ applied to an object of class “character”

Any idea on this error? it kind of the complex, I can not figure out it by myself.
Thanks. Looking forward to your reply.

2

Hi Chenx,

Can you provide a complete script for use to reproduce the issue you encountered?

Bests,
Zhiqiang

3

Dear developers，
I have the same error information. Could you tell me what the cause is and how to solve it?
Thank you very much. Looking forward to your reply！

code and error information

  • The first scenario:
    mSet<-SanityCheckMummichogData(mSet)
    mSet<-SetPeakEnrichMethod(mSet, algOpt = c(“integ”), version=“v2”)
    mSet<-SetMummichogPval(mSet, 0.05)
    mSet<-PerformPSEA(mSet, lib = “hsa_mfn”, libVersion = “current”, minLib = 3, permNum =100)

    [1] “Got 7499 mass features.”
    [1] “685 inital ECs created!”
    Error in UseMethod(“melt”, data) :
    no applicable method for ‘melt’ applied to an object of class “character”

  • The second scenario:
    mSet<-SanityCheckMummichogData(mSet)
    mSet<-SetPeakEnrichMethod(mSet, algOpt = c(“gsea”), version=“v1”)
    mSet<-SetMummichogPval(mSet, 0.05)
    mSet<-PerformPSEA(mSet, lib = “hsa_mfn”, libVersion = “current”, minLib = 3, permNum =100)

    [1] “Got 7499 mass features.”
    [1] “A total of 3092 of duplicates were merged.”
    [1] “A total of 2300 of duplicates were merged.”
    [1] “A total of 3092 of duplicates were merged.”
    [1] “A total of 3092 of duplicates were merged.”
    Error: ‘na.omit’ is not an exported object from ‘namespace:data.table’
    In addition: Warning message:
    In serialize(data, node$con) :
    ‘package:stats’ may not be available when loading

Bests,
Jing-Jing Ni

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