Hello, I am analyzing an experiment and am trying to come up with a model design to compare the differences between 2 treatments and 2 factors. I need help in trying to organize the model design matrix in EdgeR. How can I write the code for them to be recognized? I also need to make sure my replicates are similar to one another in each 'group' in order to effectively compare. I have been analyzing everything separately and then combining results, but I am wondering if there is a more efficient way to go about analyzing the data?

Factor #1 | Factor #2 | |
---|---|---|

Treatment #1 | 4 Replicates | 4 Replicates |

Treatment #2 | 4 Replicates | 4 Replicates |

The table is an overview of the data I have for the RNA-seq experiment. I am interested in any differences between all possibilities. Thanks in advance to any help offered!