I am performing a DE analysis using Deseq2. For my experimental settings, I would like to compare leukodystrophy affected patient against control patient. For each condition, I have three patients and two replicates from the same patient, with a total of 6 replicates for each condition (see Figure attached).
I am attaching also the sample distribution with PCA plots with condition variable and the information of patient
I was wondering if for this experiment it is recommended to perform a nested analysis or a “collapsed- replicates” analysis.