I am about to run Deseq2 on my featurecounts replicates.
I am looking for differential expression over a factor of time and have 4 timepoints. I kept the data for these different timepoints separate so I can add the featurecounts output for each as different factor levels. I just wanted to check what I do with replicates - I have 2 biological replicates per timepoint, and each of these biological samples was sequenced twice. So for one timepoint I have 4 sequencing files. Do I just group these 4 files together - so I would have 4 factor levels that each of 4 files? Thanks for your help!