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FrederickHuangLin / ANCOMBC

Differential abundance (DA) and correlation analyses for microbial absolute abundance data
https://www.nature.com/articles/s41467-020-17041-7
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Different results with ancombc2 depending on the order of the taxa #253

Open laetitia-schramm opened 7 months ago

laetitia-schramm commented 7 months ago

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 commented 5 days ago

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