Do we still need to normalize feature table for beta-diversity?

[junfei_guo]

Good afternoon,

I am using the Qiime 2 to analyze the beta-diversity, so just wondering if we still need to normalize the feature table before we put the data in PERMANOVA as we did in Qiime 1?

Thanks very much for the help!

[colinbrislawn (Colin J Brislawn)]

Good afternoon,

@junfei_guo

still need to normalize the feature table

Yes! And rarefaction is also possible in Qiime 2.

See this conversation here:

Feature Table Normalization Strategies in QIIME2

Hi Nate, Adding alternative normalization strategies has been on our radar for a while. We have an open issue here to track progress. We will post here with updates when those are added to a future QIIME2 release. However, non-rarefying-based normalization is built in to some QIIME2 analyses, e.g., ANCOM for differential abundance testing. So separate normalization may not be necessary (or even undesirable), depending on your goals. For now, rarefying is the only normalization method built in…

Colin

[junfei_guo]

Thank you for your response! I still got a little confused, so we can use the rarefied_table in core-metrics foe both alpha and beta diversity?

Thanks!

[colinbrislawn (Colin J Brislawn)]

@junfei_guo

so we can use the rarefied_table in core-metrics foe both alpha and beta diversity?

Correct. Or you can use the new plugins that come with Qiime 2. Like these!

https://docs.qiime2.org/2018.4/plugins/available/diversity/alpha-rarefaction/
https://docs.qiime2.org/2018.4/plugins/available/diversity/beta-rarefaction/

These plugins perform the rarefaction step multiple times, then combine the result into a unified measurement of diversity.

For PERMANOVA, you could use the rarefied table, or pass in 'ReadsPerSample' as an input to the model as another method to control for sampling depth.

Colin

[junfei_guo]

I see. Thank you so much for the explanation!

[thermokarst]

@colinbrislawn

hen combine the result into a unified measurement of diversity.

Just a quick correction here - the results are not combined in a unified diversity measurement, but rather, the impact of various rarefaction depths on diversity metrics are summarized and displayed in these interactive visualizations.

@junfei_guo

so we can use the rarefied_table in core-metrics foe both alpha and beta diversity?

The rarefied table is returned as one of the outputs from diversity core-metrics and diversity core-metrics-phylogenetic. You can also rarefy a table directly using the feature-table rarefy command.

Hope that helps!

[junfei_guo]

More clear to me, thank you very much!