Problem with Differential abundance analysis with gneiss

Hi, I tried Differential abundance analysis with gneiss in Qiime 2. However, when I looked at the regression summary, I found that one treatment group was missing. I have four treatment groups in total, but only three of them showed in "Simplicial Linear Regression Summary".
The commands I used were:
qiime gneiss ols-regression --p-formula "parity+block+Period+Treatment" --i-table RF_filtered_balances_1.qza --i-tree RF_filtered_hierarchy.qza --m-metadata-file RF_metadata.tsv --o-visualization RF_regression_summary-1.qzv
And the mapping file was loaded:
RF_metadata.tsv (33.1 KB)

Could you please help me with this problem? What the reason might be?

Thank you so much!

Junfei

Hi @junfei_guo. This is expected, due to the way that regression parameters are specified. The original explanation is here

That being said, did you have any luck looking over the previous gneiss questions? I know that there is a lot! But this has been asked a few times on the forums, so getting a better idea how to make this content more accessible could help.

Thanks for the suggestion! I found the solution in previous discussion.
However, when I looked at the results of the taxa-summary, I could not find proportion plot. I have four treatment groups in my data file, does that mean we can only get the proportion plot figure when we just have two treatment groups?

Thank you so much!
Junfei

That is correct - see this post here for reference.

Great! I saw the problem here, thanks!

Junfei

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.