**0**wrote:

Hi all,

I’m working with longitudinal data but I am not sure which is the best way to analyse this type of data using limma.

I have the blood methylation data from 24 individuals evaluated at the baseline and after 3 years of follow up. All 24 subjects were healthy at the baseline and all developed the disease after the follow-up.

I would like to compare the methylation values between these two time-points. However, I don’t know how to construct the model considering that I’m comparing the same individuals in two different moments.

I have two variables:

1) Time (baseline or follow-up);

2) Subjects (identifying the different measures for the same sample)

How is the best way to construct the model.matrix and the lmfit?

Any help would be greatly appreciated.

Thanks!