Hey @jairideout,
Can you please verify again that the filtered .qza file is filtered as expected (e.g. using qiime feature-table summarize) and then rerun core-metrics on the filtered table?
Yep, verified again and yes it was filtered properly. I even went ahead and took my filtered feature-table and exported my data as you recommended [here] (Is there any way to summarize taxa plot by category?) and then ran beta_diversity_through_plots.py on qiime 1 and my filtered samples are not there- everything looked good.
Please supply a new output directory (one that doesn't exist) to core-metrics. Do you still see the same results in the Emperor plots?```
They look about the same, but are not exact. The samples I wanted filtered include sample 29,112,46,55 and 56. When I open my emperor plot, go to the Visibility tab and click on scatter: Description I still see those samples in the emperor plot with the original NoFIlterbray_curtis_pcoa_results.qza-emperor.qzv (743.3 KB) and filtered feature-table FilteredMFbray_curtis_pcoa_results.qza-emperor.qzv (749.6 KB), but not on the emperor plot generated on qiime1.