<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>

CC BY-SA 4.0
2019-03-31T11:22:16.790Z
2019-03-31T11:22:16.790Z
Devon Ryan
<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>

<rna-seq><deseq2><limma>
How to get log2 fold change of RNA-Seq data for time series experiment?
# 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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