Could not find function "PlotOPLS.Imp" and errors with OPLSDA.Permut

MetaboAnalyst
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1

Hi,

I want to report some functions of MetaboAnalystR 3.2.0 stop working . I got errors with OPLS-DA functions: Error in PlotOPLS.Imp(mSet, “opls_imp_0_”, “png”, 72, width = NA, “vip”, : could not find function “PlotOPLS.Imp”. And also for OPLSDA.Permut function: Error in if (mSetObj$analSet$opls.reg) {: argument is of length zero. I also tried example data (MS peak intensities) and then reproduced same errors.

My analysis was run on a server (HPC system). I am not sure if it is relevant. Thank you!

Cheers

2

Hi Gong,

Thanks for reporting this issue. I have exported the function PlotOPLS.Imp. You can use it directly now.

As for the “length of zero” issue, that maybe related with the error in the previous step. Please check your steps or share a reproducible example (commands of line-by-line from the begining) with me for further checking.

Bests,
Zhiqiang Pang

3

The same problems were reported in my analysis. My platform is Win10，R 4.2.2, MetaboAnalystR 3.3.0 (also tested in 3.2.0).

Here’s my solution:

  1. PlotOPLS.Imp() still an internal function, you can use it as: MetaboanalystR:::plotopls.Imp()
  2. The value of mSetObj$analSet$opls.reg is from OPLSR.Anal(mSet, TRUE), so, add:
    mSet$analSet$opls.reg ← True