text: user1684: I know if there is one control and one treatment group it is pretty straight forward to interpret log 2 fold change. But, I have time course experiment. I have infected cells with viruses and I harvested cells at different time points: o hr, 6 hour, 12 hr and 24 hour. Here o hr is my non-infected control. What is the best way to show log 2 fold change for each gene in this type of time course experiment. I ultimate aim to find highly expressed genes at different time points. 
  
  user77: If you just want the change with time then use time as a continuous variable. The log2FC will then be the change per hour (you can use the default Wald test to extract it).
  For time-point specific comparisons you'll instead need to treat the time points as groups and use contrasts as appropriate.
  
original_text: 1684: <p>I know if there is one control and one treatment group it is pretty straight forward to interpret log 2 fold change. But, I have time course experiment. I have infected cells with viruses and I harvested cells at different time points: o hr, 6 hour, 12 hr and 24 hour. Here o hr is my non-infected control. What is the best way to show log 2 fold change for each gene in this type of time course experiment. I ultimate aim to find highly expressed genes at different time points. </p>
   77: <p>If you just want the change with time then use <code>time</code> as a continuous variable. The log2FC will then be the change per hour (you can use the default Wald test to extract it).</p>
  
  <p>For time-point specific comparisons you'll instead need to treat the time points as groups and use contrasts as appropriate.</p>
  