Gene expression was quantified before and after exercise.
Exercise was performed in two conditions: untrained and trained, but it is the same individuals in both conditions.
How do I get genes that increase/decrease more after exercise in the trained vs untrained state?
Mark! I do not want to compare «before» values between untrained/trained, only the difference of difference: (after-before)trained - (after-before)untrained
I've been trying to suggest that users not tag the names of many different methods when posting questions, as this triggers emails to all the developers involved. I understand the desire to have many developers look at your question, but it's not really support for a specific package anymore, but general strategies for analysis.
I am sorry, I didn't know!