Time-series RNA-seq analysis using DESeq2

Question

[Debebe]

Hello All,

I am working on time-series RNA-seq data. I have four individuals and collected RNA-seq samples for each individual at 4 different time points (T1, T2, T3 and T4). The experiments shown below.

SampleInfo

           Individual        Time
Sample1.1   Sample1          T1
Sample1.2   Sample1          T2
Sample1.3   Sample1          T3
Sample1.4   Sample1          T4
Sample2.1   Sample2          T1
Sample2.2   Sample2          T2
Sample2.3   Sample2          T3
Sample2.4   Sample2          T4
Sample3.1   Sample3          T1
Sample3.2   Sample3          T2
Sample3.3   Sample3          T3
Sample3.4   Sample3          T4
Sample4.1   Sample4          T1
Sample4.2   Sample4          T2
Sample4.3   Sample4          T3
Sample4.4   Sample4          T4

I would like to identify differentially expressed genes across all time-points.

For that I use the LRT test and the following model

dds <- DESeqDataSetFromMatrix(countData = counts,
           colData = SampleInfo,
           design= ~Time)
dds <- DESeq(dds, test="LRT", reduced=~1)

If I want to identify differentially expressed genes over all time-points, how does it look the above design model.

Thanks!

[bk11]

Please check the link below. Similar query had been discussed earlier-

Using DESeq2 for time-series analysis