Different results with ancombc2 depending on the order of the taxa

[laetitia-schramm]

Hi, I have an issue regarding ancombc2 function. I am working with taxonomic data from metaG and metaT sequencing. I created a phyloseq object and used it as the input data for ancombc2. However, I realised that, depending on how the taxa are ordered in my phyloseq object, I obtain different results (significant taxa). The data is exactly the same (same taxa, same counts, same samples, etc...), just the order changes and I used the exact same formula and the exact same seed number before running ancombc2. I also made sure that everything matches between the otu_table, sample_data and tax_table in my phyloseq object (making sure that groups were properly assigned to the right samples, etc...).

I was wondering if the order of the features tested matters for the statistical test, which could explain the difference in the obtained results?

Thanks in advance for your help!

[Maggie8888]

Thanks for your question. Could you please provide more details of your data?