"Calculate.ANOVA.posthoc" not ound error

MetaboAnalyst
1

Hello dear MetaboAnalysome,

Did anyone, when trying to run MetaboAnalystR, encouter the error :

mSet<-Calculate.ANOVA.posthoc(mSet, “fisher” , 0.05)
Error in Calculate.ANOVA.posthoc(mSet, “fisher”, 0.05) :
could not find function “Calculate.ANOVA.posthoc”

As all functions in the stats_univariates.R file are tracable except this one.
Ps: I dont have more than 1000 significant features.
I use R-4.2.3 version.

Thanks.

2

Maybe try to re-install the package. The function is clearly in this file: stats_univariates.R

1 Like
3

I had the same error.

2 Likes
4

I reinstalled, fruitlessly, the pacakage locally and with devtools.

It might have something to do with the (.on.public.web) condition, which is in the end of some functions, even though it’s handeled by the .get.mSet function.

Strangely, I still dont understand why it doesn’t work, and why the function Calculate.ANOVA.posthoc is not listed when I run lsf.str(“package:MetaboAnalystR”).

5

We are in the process of upgrading the server and then the R package. Maybe you can try the shortcut for now:

source(“PATH TO THE FILE CONTAINING THIS FUNCTION”)

6

Hello,

I downloaded the stats_univariates.R file and executed it using the source function. After that, I ran
Calculate.ANOVA.posthoc. However, I encountered the following error:

source(file.choose())
mSet ← Calculate.ANOVA.posthoc(mSet, “tukey”, 0.05)
Error in .get.mSet(mSetObj) : could not find function “.get.mSet”

I am not very familiar with programming, so there’s a possibility that I might have done something different from what you intended. Could you please advise on how to resolve this issue?

Thank you.

7

I get the same
Error in .get.mSet(mSetObj) : could not find function “.get.mSet”
when I try to do “PlotPCAPairSummaryMeta”. I saved the source for this function and I source it to R and I get the above error when I try to run it.
BR, Pezhman

8

The “source” is a hackish approach, as it will potentially interrupt the normal workflow. I mentioned this assuming you are very familiar with R and our code is open.

You either use our web-based platform (primary), or try to use the standard R commands after proper installation of MetaboAnalystR package. Note our support for R is limited due to time.

Final note - troubleshooting requires reproducible example, not just the last error message. This is described clearly in our post guide.

9

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