**0**wrote:

Hi, I'm having a hard time to understand how design matrices works in linear models.

From limma users guide:

` WT MUvsWT `

`Array1 1 0 `

`Array2 1 0 `

`Array3 1 1 `

`Array4 1 1 `

`Array5 1 1`

I do not understand how the coef WT (intercept) can be the average expression for the WT if it has a value of 1 even for those that are MU. Could someone explain me how to interpret this intercept? In theory I understand what the intercept is, but I don't understand how this vector capture the mean log expression for the first factor (WT) if the value is the same for every sample. Where the information about the levels are in this vector?

Thank you.

**25k**• written 2.4 years ago by marconerdaum •

**0**