how to do the alpha diversity analysis seperately

Hello everyone, I am a newer for Qiime2, and moved forward with the forum support. Now I have some alpha diversity results but could not understand. The following is one of the results.

The above figure shows no significant difference in statistically between two treatments, which is meaningless. Because each treatment inculdes two genetic lines. I hope to obtain two alpha diversity results between genetic lines in each treatment. How to do it? Should I seperate the metadata file according to the treatments at the beginning, then proceed the analyzing pipline two times?

sample-metadata.tsv (3.8 KB)

I am really appreciated with your help.

Hi @terren,
The alpha diversity group significance test is basically going to take every unique value in your metadata columns that are categorical and treat those as your groupings. So if you have a 2 treatment x 2 genetic line set up, you could add a new column in your metadata file that describes your samples with 4 unique values, so for example Control_WT, Control_KO, PBS_WT, PBS_KO. Then repeat alpha diversity group significance and select this new column to see 4 groups being compared to each other.

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Thanks very much. After adding a new colomn, I am wondering whether I should just repeat the alpha diversity group or reanalyze from demultiplexing the reads ?

Hi @terren,
The metadata file can be changed without needing to re-process your reads, the change here really only affects the tests that call on that specific new column. So, only re-run the diversity-alpha-group-significance test.

I have re-run the alpha diverstiy analysis scripts.I am really appreciated with you.

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