I want to ask regarding time course data. The data I want to analyse is from human iPSC cell reprogramming with time course data from mature cell induce with Yamanaka factor to become iPSC with several time steps. What are the best ways to do this?
Firstly, I am thinking to use CPM as a measure whether a gene is expressed or not and check for each time point. I think of this because maybe DESeq2 will not be able to count the log fold change if in one time point the expression is almost zero. Will DESeq2 handle this too so that I can just use DESeq2 directly?