Using Songbird DIfferentials in Qurro

Hello,

I wanted to get some clarification on the suggested differential to use for plotting features in Qurro. The formula I used for songbird had a variable of ‘facility’ which contained three groups. The songbird model created differentials for the intercept, facility(T:2), facility(T:3). My understanding of the differentials is that the intercept are the zero interactions, and the others are facility 1 as the reference compared to facility 2 and 3, respectively. My question is, when manipulating the plot in qurro to look for differential abundant taxa between my facilities, should I use the intercept differential or the facility(T:2) and facility(T:3) differentials?

Thanks,
Zach

The formula I used for songbird had a variable of ‘facility’ which contained three groups. The songbird model created differentials for the intercept, facility(T:2), facility(T:3). My understanding of the differentials is that the intercept are the zero interactions, and the others are facility 1 as the reference compared to facility 2 and 3, respectively.

That interpretation sounds right, assuming your formula was something like "facility" or "C(facility, Treatment('1'))" or something like that. If you haven’t read it already, this section of the Songbird README describes how to set your reference manually (in case, say, you’d prefer to have facility 2 as your reference).

My question is, when manipulating the plot in qurro to look for differential abundant taxa between my facilities, should I use the intercept differential or the facility(T:2) and facility(T:3) differentials?

The latter—facility(T:2) and facility(T:3). In general, I don’t recommend using the intercept differential in Qurro (I know it’s the default option, sorry… changing that is on my TODO list). For looking at differentially abundant taxa between facility 2 and the reference facility (facility 1), you should be able to use the facility(T:2) differential, and for looking at differentially abundant taxa between facility 3 and 1 you can use facility(T:3).

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Thanks @fedarko, that helps a lot!