I know there are a lot of questions asking similar things here on this forum and I checked the vingette and did a lot of other research but I still have a hard time wrapping my head around it.
I have multiple cell lines, multiple time points and multiple treatments:
Cell lines: CL1, CL2, CL3 Time points: 6h, 24h Treatments: T1, T2, T3, Control
For each cell line and each time point, there are 3 different treatments plus a control. 3 replicates for each sample -> 72 samples I want to measure control vs each treatment at each time point in each cell line. No testing across time points or across cell lines. My first thought was to separate the data into 6 different data sets (CL1, 6h | CL1, 24h | CL2, 6h | CL2 24h | CL3, 6h | CL3, 24h) and simply do the DE analysis separately, but I read that this is not the way to go. In the end it would also be nice to get a normalized count matrix with all data normalized together, for PCAs and similar.
I hope I made it understandable. How do I design the DESeqDataSet?