Songbird interpret differentials - Intercept

[Boris_Martin_Tangoa (Boris Martin Tangoa Mesia)]

Hello community. I was using Songbird to analyse my data and i have a question when looking at the differentials table.
I understand that the differential refers to the logarithm of the fold change in abundance of a taxa between two conditions. I understood that two conditions in my case would be "treatment vs control", as i set the control as intercept. And that if it was negative, the abundance in the treatment decreases when compared to the control, and that if it was positive, the abundance in treatment increase when compared to control.
So my question is, why is there a Intercept column with different logarithms, and how do i interpret these values?

You can see my differentials table attached belowed.

metadata.tsv (94.6 KB)

[mortonjt (Jamie Morton)]

Hi @Boris_Martin_Tangoa there are a couple of posts on this that may help with understanding this

Songbird intercept and differentials interpretation in multivariable model

I have a question regarding the intercepts and differentials I got from Songbird using the following formula "C(Sampletype, Diff, levels=['3', '2', '1'])+Penstyle" I have three sample types (1, 2, 3) and two pen styles (old and new). The way the formula is written, sample type 1 and new pens are the reference. In this way, there are differentials created for sample types 2 and 3 and old pens. I understand how to interpret the intercept and differentials in cases that only look at one categoric…

Songbird interpret differentials - Intercept

Hello community. I was using Songbird to analyse my data and i have a question when looking at the differentials table. I understand that the differential refers to the logarithm of the fold change in abundance of a taxa between two conditions. I understood that two conditions in my case would be "treatment vs control", as i set the control as intercept. And that if it was negative, the abundance in the treatment decreases when compared to the control, and that if it was positive, the abundance…

The intercept is just the (centered) mean log abundance of the control group. We need this in order to the regression, but is is probably not useful for interpretation.