Continuing the discussion from Metaboanalyst-Pathway Analysis- using default terms and Oryza Sativa as organism:
I have been using this tool to interpret the dominant pathways associated with my maize root metabolomic study under drought (dehydration stress). I am using the default terms. For Pathway impact calculation, the default term is relative betweenness centrality. Please suggest what I should use if I want to compare the overall metabolomic pathways affected by drought in two different genotypes.
Additionally, please advise whether it is necessary to consider all three p values (i.e., -log10 p value, FDR, and Holm P) being less than 0.05 or 0.1 to deem a pathway as significant.