What does it mean negative LDA scores?

Downstream analysis and statistics LEfSe
1

Hello,
I understand that LDA score is the degree of the difference in the relative abundant of features when comparing two groups (A vs. B). For example, positive LDA values mean that there is an increase in the relative abundance of that particular feature in the group A with respect to the group B. For negative LDA values, does it mean that the feature showed a decreased relative abundance in the group B with respect to the group A?

Galaxy8-C)_Plot_LEfSe_Results_on_data_7
Galaxy8-C)_Plot_LEfSe_Results_on_data_71050×907 70.1 KB

Thanks,
Juliana

2

Hi Juliana,
Yes, your interpretation is correct. When comparing two categories, the plots give positive LDA scores for one category and negative for the other. If you were to compare 3 or more categories, they would each be positive, and color-codeed by the group where the abundance is highest.
I hope that helps!
Best,
Meg

3

What would all the positive LDA scores imply if there are three or more categories? Would the scores demonstrate only where the abundance is highest?