I am not a statistician so apologies in advance if my question is naive. This is a more a methodological question, than a specific issue with code. I am dealing with data from a bulk RNASEq experiment with cells grown in different environments, treated with different agents at different concentrations and in different combinations of single cell cultures, co-cultures and triple co-cultures. . My question is to do with the design formula for DeSeq2. I have a number of comparisons to make. These comparisons can be single factor and or additive between various combinations of the factors. My question is would I need to make a new design formula and re-run the Deseq2 process each time for each unique comparison, or can I code up the distinct groups as a single factor and use that as the design for every comparison that I need to make. Which of these two approaches could be considered best practise?
Thanks in advance,
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