ALDEx2 for three more groups adjusted for longitudinal study design

Community Plugin Support
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Dear qiime2 developers,
I would be so happy if you apply aldex.glm module for q2-aldex2 plugin for 3 more groups and longitudinal study design. I wonder if it’s possible to calculate effect size during the analysis.
Thanks a lot

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Welcome to the forum @Genebio!

I have moved this to the “community plugin support” and am notifying @dgiguer of your request and question. Thanks!

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3

Hi @Genebio,

Thanks for the feedback! We are working on implementing the glm module. The current work around is to use the R package.

Cheers,

Dan

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Hi @dgiguer,

When will aldex.glm module be included in q2aldex? Until that time, would you please explain what is the inputs to create a model matrix to use it with aldex.clr?
As ALDEx2_vignette states, I need a RangedSummarizedExperiment object and vector containing a descriptor for the samples. I have ASVs table and metadata file for three groups.
My questions are, how can I convert them to dataframe of reads, do I need to merge them?
what are the covariates and mm in the documentation mean? Are they corresponding to the vector of conditions(condos)? Please excuse my shallow knowledge and would appreciate if you provide any tutorial or link can help when working with more than two groups.

Regards,
Maysa