Linear mixed effect models using taxa relative abundance table?

[idapantoja]

Hi all,

I want to use the Linear mixed effect model test for my data. But I was wondering if instead of using the diversity file (like in the tutorial example that used shannon.qza) use the taxa relative abundance table. Can I modify the command for relative abundance?

Thanks!
Ida

[Nicholas_Bokulich]

Sure you can:

$ qiime longitudinal linear-mixed-effects --help
Usage: qiime longitudinal linear-mixed-effects [OPTIONS]
...
  --i-table ARTIFACT PATH FeatureTable[RelativeFrequency]
                                  Feature table containing metric.  [optional]
...

so you can input a relative frequency feature table, and for the metric parameter you would enter the name of the taxon of interest (the full name, exactly as it is written in the feature table).

Good luck!

[idapantoja]

Great news!

And that would be a .tsv format? biom?

Thanks!
Ida

[Nicholas_Bokulich]

@idapantoja

And that would be a .tsv format? biom?

The help docs say it all:

@Nicholas_Bokulich

$ qiime longitudinal linear-mixed-effects --help
Usage: qiime longitudinal linear-mixed-effects [OPTIONS]
...
  --i-table ARTIFACT PATH FeatureTable[RelativeFrequency]
                                  Feature table containing metric.  [optional]
...