Question: Deal with the time-course RNA-Seq datasets
gravatar for wangdp123
13 months ago by
wangdp123240 wrote:

Hi there,

I have a set of time-course RNA-seq datasets.

The experiment design is as follows:

1. For each condition, there are 3 replicates.
2. In total, there are 5 time points: T0; T1; T2; T3; T4.

I notice that there is a tutorial from this website ( that explains how to perform time-course analysis for a control and treatment time series.

However, in my case, there is no control-treatment. I wonder how to make the design in DESeq2 right and if there is a need to consider the replicates as a variable in the design?

Many thanks,


rna-seq time-course • 371 views
ADD COMMENTlink modified 13 months ago by andrew.j.skelton736.0k • written 13 months ago by wangdp123240
gravatar for andrew.j.skelton73
13 months ago by
andrew.j.skelton736.0k wrote:

If all you're interested in (or have to work with), is the differences between time points, then that's all you can test in your experiment. Section 9.6.1 of the Limma users guide is a good basis to start from. These principles can be applied to DESeq2 too. There are other ways to look at your data, including using time as a linear variable, or splines... but for now differential expression between time points is the best starting point.

ADD COMMENTlink written 13 months ago by andrew.j.skelton736.0k
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