I apologize for a second post but I want to bring this questing back up as I still cannot find a definitive answer on my own (Moderator: previous post was Repeated Measures mRNA expression analysis I ). In brief, I am wondering about the design matrix when testing for differential expression between two groups within which each sample has been measured at consecutive timepoints (repeated measures). Therefore, if my interpretations are correct, I need a two-way analysis that recognizes dependence between consecutive measurements. I am familiar with limma, edgeR and DESeq but am uncertain how to design an appropriate design matrix for these comparisons. The best I can guess is that I add a 'Subject' factor to the design matrix corresponding to each unique sample to correct for dependence, is this correct?
My sincere regards,
Integrated Biosciences PhD Candidate
University of Minnesota