I have RNA-Seq, time series data from six conditions and five time points (i.e. 1h, 2h, 12h,24h, 48h). The conditions are the following:
WT (as Control)
I want to run a differential analysis per time point using limma, using the WT as a control in each respective time point.
My design matrix is specified by
design <- model.matrix(~ 0 + fac)
fac is a factor combining Mutant_Timepoint (Mut1_1h, Mut1_2h, ... , Mut1+3_24h, Mut1+3_48h)
Would there be any difference between using limma/voom with time series and the Time course section in limma's users guide? If yes, which one would be the most appropriate?
Thank you in advance for the help.