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:
However, if the same subjects were used across time then I wanted to confirm
- should the design matrix for matched samples in a time series experiment be:
> design <- model.matrix(~subjectID+Group)
- any change to setting up contrasts for pairwise comparisons against baseline (T0) for each condition and between time points?
Appreciate all the help.