I am relatively new to working with RNA-Seq data and have longitudinal data from participants measured at baseline and various follow-up time points. My question is: Is it possible to use the count data (after normalization) to calculate a change score (delta) for each transcript for each participant, comparing the baseline to a specific follow-up point? I am performing time point comparisons using the data as it is. However, I would like to test associations between changes in continuous clinical variables and changes in gene expression (by using the change scores/deltas). I understand that there are several limitations to this approach, but I am wondering whether the change score calculations are feasible at all when working with count data.
