I have RNA-seq data for a time-course experiment which consists of the same starting and end points but two different conditions: https://postimg.cc/DW0RzJf1
I am unsure how to correctly model the data to answer the following questions:
- Identify differential genes between each time-point within each condition
- Identify differential genes between conditions within each time-point
To answer each question respectively I thought about doing the following:
- Subset the data by condition and identify differential genes separately using a formula such as: ~ Time.
- Remove the start and end points entirely and model the data using a simple formula such as: ~ Time + Treat)
Would this be an appropriate design? I'm concerned about subsetting the data too much because it will affect the estimation of variance e.t.c