First time using ANCOM and I’m trying to diagnose some funny results. In looking at the ‘ancom.csv’, I am seeing 0 for all the values in the ‘W’ column, and False for all the values in the ‘Reject null hypothesis’ column.
I am using the Python implementation and running it as such:
from qiime2.plugins import composition
pseudo_counts = composition.methods.add_pseudocount(table=q_table)
ancom_well = composition.actions.ancom(table=pseudo_counts.composition_table,
and then looking at the …/data/ancom.csv file to get the values out. The ‘q_table’ variable is created from a pandas DataFrame with samples by features as the values, which is then passed to the qiime2 Artifact import_data function. ‘q_metadata’ is created from passing the sample metadata DataFrame with one specific column to the MetadataCategory constructor.
If anyone could provide some insight into these results, that would be very helpful. Hopefully, I didn’t introduce a bug somewhere!
Unfortunately I cannot share the actual data due to confidentiality.
Thanks in advance!