How to convert peak intensity to compound names

MetaboAnalyst
1

I used MetaboAnalystR package to process my raw data.
and the package output 2 csv files as “metaboanalyst_input.csv” and “annotated_peaklist.csv”
After getting these 2 files, I upload “metaboanalyst_input.csv” to MetaboAnalyst 5.0 website ----> statistical analysis(one factor) and output the OPLS-DA VIP results.

opls_imp_0_dpi72
opls_imp_0_dpi72576×576 26.6 KB

But I have problem with coverting the value to compound names
Is anyone know how to deal with it?

2

The statistical analysis modules do not perform any annotation - whatever ID types you upload are the ones displayed in the results.

Since you are already in R, I suggest using the ‘merge’ function to re-label your numerical peak IDs with the compound names. Then, if you analyze this labeled table in MetaboAnalyst, you will get the results with the compound names.

3

Thanks for your good advice.
But I can not find the “merge” function in metaboAnalystR package, is there any code available to map the peakIDs with the compound names?

4

merge() is a very common function in base R, so you do not need to load any special libraries to use it. Here is a tutorial on how to use it.

5

Thanks a lot! After I merge the data below, I got the file named “compound_db.qs”
annotated_peaklist.csv (1.4 MB)
metaboanalyst_input.csv (664.8 KB)

However, after searching many websites, I can’t find the way to process this file to do further analysis

6

You should search how to load a .qs file into R. There is a library for it.

It seems that you are not so comfortable using R - in this case, I suggest that you mainly use the web version of MetaboAnalyst, or take some introductory course to programming in R. There are many good tutorials online.