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!