I was wondering if someone could explain what the "linear modelling" part in Limma (linear models for microarray data) does. I've done a lot of reading in manuals already and nowhere it seems to make me understand what is done and why.

The manual says this:

*You have to start by fitting a linear model to your data which fully models the "systematic part" of your data*

And I learned that a linear model is constructed for each gene

The question that I have is, what does this model look like and what is 'plotted' in this model, for example what is on the X- and Y-axes? I can't seem to find it anywhere.

Thanks in advance,

Christian