Hi @nricks,
@mortonjt will be able to explain this much better than me but if I had to guess I would think the results you are seeing in your 2nd location (with low W values) is likely a result of large rare features from that site. See this explanation of how the W values are determined. With lots of rare taxa that only appear in a few samples, it’s likely that ANCOM is under performing due to violations of the recommended guideline where less than 25% of the features are expected to be different across groups.
I think a first good step is to reduce noise from your feature-table by getting rid of rare and low abundant features that only appear in a few samples or that they make up a very small portion of the features.
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