I have a basic question regarding the normalization of RNAseq data - I understand why we have to normalize the raw counts, but I do not fully understand the biological details and I am confused about the differences between methods - so sorry if the answer is obvious.
Basically, I have ~ 58.000 transcripts, and I just want to normalize the raw counts and transform them so that I can make comparisons (I have 2 time points and 60 samples per time point). I would like to do it in R.
My question is: Is there an opportunity to just normalize & transform (I mean sth like (log)CPM) my data, without a prior filter? If yes, do you have any suggestion what method/ package (and function) I could use?
(I would like to filter and apply a variance-mean stabilization afterwards)
Thank you for advices!