# 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!