SanityCheckData failing

MetaboAnalyst
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1

Hello!
I’m just starting out using MetaboAnalystR, so please bear with my level of beginner-ness. I’d love to get it to work because it’s really perfect for my research purposes.

I want to run a pathway analysis. I’ve imported my data and have tried multiple times to run the following:

mSet ← InitDataObjects(“conc”, “msetora”, FALSE)

mSet$dataSet$orig ← t(my_data)
mSet$dataSet$cls ← cls$Class
mSet$dataSet$type.cls.lbl ← “disc”
mSet$dataSet$format ← “rowu”

mSet ← SanityCheckData(mSet)
mSet ← ReplaceMin(mSet)

I get as far as mSet ← SanityCheckData(mSet), and then I get a vector of 0, which in my understanding means it failed. I’ve tried multiple things including restarting R, reinstalling MetaboAnalystR, removing all NAs from my data, checking for duplicates in names of variables, checking that my class labels are correct and the same length as the number of columns, and this all seems to be correct. After that I also ran the same code with synthetic data and even that returned a 0 vector, so the problem doesn’t seem to be in my data.
I’m working in RStudio version 4.4.0 on Windows 10.

Has anyone run into this issue, and do you have any suggestions I might try, or even reasons this command might fail? Would be great to get this to work. Thank you!

2

If you are new to MetaboAnalystR, please use our web-based platform which is designed for people to focus on data analysis, rather than learning R.

You can also learn the proper R commands for data analysis using the “R Command History” panel on the web site. For pathway analysis, here are the top three commands

|1.|mSet<-InitDataObjects(“conc”, “pathqea”, FALSE)|
|2.|mSet<-Read.TextData(mSet, “Replacing_with_your_file_path”, “rowu”, “disc”);|
|3.|mSet<-SanityCheckData(mSet)|
|4.|mSet<-ReplaceMin(mSet);

The issue is that you did not follow the procedure after Step #1 …