ANCOM-BC interpreting results

[fl-saravia]

I am using ANCOM-BC to identify discriminatory taxa from shotgun metagenomic data (analyzed with Metaphlan4). I can successfully run ANCOM-BC but am still confused about results interpretation, specifically LFC.

I know that your github page answered the primary results for LFC (question 3) but I am still struggling to understand.

3. Q: In the primary results, what do lfc_(Intercept), lfc_groupB, and lfc_groupC represent if I have a group variable with categories A, B, and C?
   A: In the primary results, the terms lfc_groupB and lfc_groupC represent the log fold changes (logFC) relative to the reference group, which is group A by default. These logFC values indicate the difference in abundance between group B and group A, and between group C and group A, respectively.
   On the other hand, lfc_(Intercept) refers to the log fold change of the grand mean, which may not be a parameter of particular interest in this context.
   It's worth mentioning that if you wish to change the reference group, you can use the factor function in R to rearrange the levels of the group variable accordingly.

If I am looking at lfc_groupB, this is the difference between group B and group A where group A is the reference group. So does a positive LFC indicate increased abundance in group A and negative LFC indicate decreased abundance in group A; another way of saying it is positive LFC is discriminatory for group A while negative LFC is discriminatory for group B?