Hey everyone,
I am new to metabolomics but was tasked to do MSEA using metaboanalyst ( Quantitative Enrichment analysis).
In my data, I have two conditions; let’s call them control vs. treated.
I am having trouble understanding the results:
Enrichment ratio: the number of hits within a particular metabolic pathway divided by the expected number of hits.
Is it in the control? In treated? In the difference between them? I am so lost.
You also get a table with the Metabolite set with P-values, FDR, etc. But how can I know which pathway is upregulated in which condition?
I understand this is a complex topic, and I appreciate your patience navigating it. I’ve tried to find answers online, but I’m still struggling to understand the concept of a ‘perturbed’ pathway.
I would be delighted if you could help.