title: How to get meaningful results from ANCOM using phyloseq object in R?
body: <p>I'm struggling to get an output that is meaningful using ANCOM to analyse microbiota.</p>
  <pre><code>out = ancombc(phyloseq = excluded_data1, formula = &quot;Status + Treatment + Time.Point&quot;, 
                p_adj_method = &quot;holm&quot;, zero_cut = 0.90, lib_cut = 1000, 
                group = &quot;Status&quot;, struc_zero = TRUE, neg_lb = TRUE, tol = 1e-5, 
                max_iter = 100, conserve = TRUE, alpha = 0.05, global = TRUE)
  
  res = out$res
  </code></pre>
  <p>Sample of output:</p>
  <pre><code>                            Status1   Treatment1   Treatment2   Treatment3  Time.Point1
  k__Bacteria_unclassified 0.49200069 8.931600e-02 0.5338123768 0.0307919322 3.292303e-01
  p__Actinobacteria        0.54382567 4.067132e-01 0.6620561010 0.5197614388 4.106100e-01
  p__Bacteroidetes         0.78646572 7.563807e-01 0.6033916623 0.2611763630 4.565237e-01
  p__Deferribacteres       0.60055702 5.411246e-01 0.9101333145 0.1253524369 5.853835e-01
  </code></pre>
  <p>The phloseq object is defined and I have used it for other analyses and filtered down, but the groups in &quot;Status&quot; should be &quot;Control&quot; and PNS&quot;, for Treatment they should be &quot;None&quot;, &quot;CS&quot;, &quot;AB&quot;,.. and &quot;Time.Point&quot; should be &quot;Before&quot; and &quot;After&quot;.</p>
  <p>How do I get results that actually tell me the comparisons between e.g. &quot;None&quot; and &quot;AB&quot;, rather than Treatment1 and Treatment2? I have no idea what Treatment1 is mapped to.</p>