May I know which metabolites should be entered to MSEA software compound list?
I want to use MSEA to find pathways that are impacted by my experiment treatment (vitamin intake). I have a list of 40 metabolites impacted by the vitamin, all with significant p-value (from ANOVA test). However, only 10 out of 40 have VIP score, more than 1.
To have the correct analysis should I enter the list of 40 or 10 metabolites on MSEA?
Thank you so much for your help.
There is no hard rules here. MSEA aims to find enriched functional themes from a list of metabolites, and it is up to you to define the list (as long as you can justify). In this case, ANOVA or VIP are both reasonable.
For exploratory analysis, you should try both - they are different methods (univariate vs multivariate) and may yield complementary insights
Thank you so much for the reply!