# MaAslin2 Interactions with Gender and Trial

**URL:** <https://forum.biobakery.org/t/maaslin2-interactions-with-gender-and-trial/4628>\
**Category:** MaAsLin\
**Created:** [January 10, 2023, 2:29pm UTC](https://forum.biobakery.org/t/maaslin2-interactions-with-gender-and-trial/4628 "2023-01-10T14:29:07Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![cassandraregine](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/cassandraregine/32/2514_2.png) [@cassandraregine](https://forum.biobakery.org/u/cassandraregine)\
**Post date:** [January 10, 2023, 2:29pm UTC](https://forum.biobakery.org/t/maaslin2-interactions-with-gender-and-trial/4628/1 "2023-01-10T14:29:07Z")

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Hello,

I have a data set that includes pre/post sequences (for which I termed the “trial” variable). MaAslin2 was a great tool to check for differences following the trial. However, I also want to look at gender differences as an interaction with the trial (so not just the overall difference in gender, which I believe would clump my pre/post data together).

I believe I would want an interaction term (am new to this kind of analysis). Am I correct in thinking that adding “Trial” and “Gender” as fixed effects would not give me the output I am looking for? I am having a hard time understanding the interaction tutorial.

Thank you!

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**Author:** ![andrewGhazi](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/andrewghazi/32/2950_2.png) [@andrewGhazi](https://forum.biobakery.org/u/andrewGhazi)\
**Post date:** [January 10, 2023, 3:21pm UTC](https://forum.biobakery.org/t/maaslin2-interactions-with-gender-and-trial/4628/2 "2023-01-10T15:21:57Z")

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You want an interaction effect if the _combined_ effect of gender and trial goes above and beyond the effect of changing them individually. Simulated explanatory example:

 ![effects](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/6/655e073a76c8c89f9d92ece20b0be1222c481ea2.png)

If you decide you want to include an interaction variable, the `model.matrix()` function in R can help set up the necessary metadata variables. Something like `model.matrix(~gender*trial, data = d)` in your case.

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**Author:** ![himel.mallick](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/himel.mallick/32/1757_2.png) [@himel.mallick](https://forum.biobakery.org/u/himel.mallick)\
**Post date:** [January 10, 2023, 3:28pm UTC](https://forum.biobakery.org/t/maaslin2-interactions-with-gender-and-trial/4628/3 "2023-01-10T15:28:54Z")

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On top of what @andrewGhazi said, once you create the interaction variable, you need to supply both the main variables as well as the interaction variable to MaAsLin 2 as fixed effects. You may want to subset your results table to the interaction term only and re-compute the q-values to reduce the burden of multiple testing but the above strategy should give you what you are looking for.

All the best,  
Himel

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**Author:** ![cassandraregine](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/cassandraregine/32/2514_2.png) [@cassandraregine](https://forum.biobakery.org/u/cassandraregine)\
**Post date:** [January 18, 2023, 4:36pm UTC](https://forum.biobakery.org/t/maaslin2-interactions-with-gender-and-trial/4628/4 "2023-01-18T16:36:35Z")

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Hello,

Thank you both for your help! I did have a followup questions. When I use the interaction terms, in my case it ended up being this,

fixed\_effects = c(“SexMALE”, “TrialPRE”,“SexMALE:TrialPRE”),

only SexMALE and TrialPRE ended up in the results. Am I miss understanding or should the interaction be included in the results?

Thanks again,  
Cassie

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**Author:** ![andrewGhazi](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/andrewghazi/32/2950_2.png) [@andrewGhazi](https://forum.biobakery.org/u/andrewGhazi)\
**Post date:** [January 19, 2023, 3:25pm UTC](https://forum.biobakery.org/t/maaslin2-interactions-with-gender-and-trial/4628/5 "2023-01-19T15:25:42Z")

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You need to make sure the interaction metadata variables are in your input metadata. Example from the Maaslin2 tutorial: [MaAsLin2 · biobakery/biobakery Wiki · GitHub](https://github.com/biobakery/biobakery/wiki/MaAsLin2#4-advanced-topics)