Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-03-31T11:22:16.790Z
Answers.LastActivityDate: 2019-03-31T11:22:16.790Z
Answers.UserDisplayName: Devon Ryan
Body: <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>
  
Tags: <rna-seq><deseq2><limma>
Title: How to get log2 fold change of RNA-Seq data for time series experiment?
ThreadText: # How to get log2 fold change of RNA-Seq data for time series experiment?
  
  (Asked by: username_0 on 2019-03-30)
  
  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.
  
  **Tags:** rna-seq, deseq2, limma
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2019-03-31. Score: 3
  
  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.
  
  
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