Hi all, I have some RNA-Seq data: 4 reps per sample, 4 different genotypes & 9 time points = 144 data points I want to essentially know the best method to normalize across ALL time points and for each INDIVIDUAL genotype. Is the state of the art normalization method today, TMM? If yes, is TMM step-by-step procedure available any where? (I do some Perl scripting, but I am pretty new to R) I realize that edgeR might be using TMM for pair-wise comparison, but I need to perform normalization across time points for each genotype. Irrespective of normalization strategy, will I have to choose the base level sample aka reference for normalization? Or can normalization be done independent of an overtly defined reference state? - I know this is a naive question, sorry... (If required, I would use time point zero as my reference state) Thanks in advance for guiding me AKSR