Hi,

I am interested in using edgeR for DE analysis of longitudinal data. The edgeR manual section 3.3.1 explains how to perform a time series analysis for two conditions at different time points. The design matrix used in the example is:

> design<-model.matrix(~0+Group)

However, if the same subjects were used across time then I wanted to confirm

1. should the design matrix for matched samples in a time series experiment be:

   > design <- model.matrix(~subjectID+Group)
   

2. any change to setting up contrasts for pairwise comparisons against baseline (T0) for each condition and between time points?

Appreciate all the help.

Thanks

Each subject receives all treatments, then you could use

model.matrix(~0+Group+SubjectID)

and the contrasts would be exactly as in Section 3.3.1.