Hi,
Metabolomic data can (and should) be analyzed as any other omic data. Articles about proteomic and transcriptomic data analyses should be applicable (sorry, I do not have specific examples to share). Depending on your level of comfort with JMP, the following may be too simple or too complex.
- To start, you may need to transform your intensities/Area under the Peak in Log format.
- When working with log-transformed data, the relative fold changes between conditions and a reference condition can be calculated as the difference between those. Note that a tall data format (all data stacked) can speed up this basic calculation.
- The Graph Builder Heat Map display can be useful for showing overall trends, but be aware that very large data sets (e.g., primary data) can stall the Graph Builder app.
- You may want to explore the data using Principal Component Analysis to assess if there are obvious groups in the data that may indicate batch effects or other dominant trends.
- In terms of analyses, I tend to use the Fit model with some JSL coding to iterate across the different analytes. In this case, a wide data format is preferable where the cases/conditions are in rows, and the analytes are in columns.
Considering the breadth of possibilities regarding analyses, proposing direct solutions to your problem is rather challenging. I recommend writing an analysis plan to define your questions (e.g., which metabolites are differentially modulated between Condition A and B) and then seek specific help with those analyses.
Best,
TS
Thierry R. Sornasse