time-series analysis with DESeq2

Question

[arshad1292]

Dear all,

I have a readcount data at 4 time points (T0, T8, T16, T24), two region (left and right) and three phenotypes (control, resilient and susceptible). I want to conduct time-series analysis to see the effect of phenotype over time in two different regions.

I have seen DESeq2 manual for time-series analysis where it suggest using LRT for this analysis but honestly I don't understand how to proceed as it lacks all the detail... like no R code is provided and it just gives a description about LRT etc.

Could anyone please help me how can I proceed. I need R code for this analysis to run it in my R terminal. There is no much material available online for time-series analysis.

Many thanks,

please see below my experimental design.

samples time    region  phenotype
T0_1    T0  left    control
T0_2    T0  left    control
T0_3    T0  left    control
T0_1    T0  left    resilient
T0_2    T0  left    resilient
T0_3    T0  left    resilient
T0_1    T0  left    susceptible 
T0_2    T0  left    susceptible 
T0_3    T0  left    susceptible 
T0_1    T0  right   control
T0_2    T0  right   control
T0_3    T0  right   control
T0_1    T0  right   resilient
T0_2    T0  right   resilient
T0_3    T0  right   resilient
T0_1    T0  right   susceptible
T0_2    T0  right   susceptible
T0_3    T0  right   susceptible
T8_1    T8  left    control
T8_2    T8  left    control
T8_3    T8  left    control
T8_1    T8  left    resilient
T8_2    T8  left    resilient
T8_3    T8  left    resilient
T8_1    T8  left    susceptible 
T8_2    T8  left    susceptible 
T8_3    T8  left    susceptible 
T8_1    T8  right   control
T8_2    T8  right   control
T8_3    T8  right   control
T8_1    T8  right   resilient
T8_2    T8  right   resilient
T8_3    T8  right   resilient
T8_1    T8  right   susceptible
T8_2    T8  right   susceptible
T8_3    T8  right   susceptible
T16_1   T16 left    control
T16_2   T16     left    control
T6_3    T16 left    control
T16_1   T16     left    resilient
T16_2   T16 left    resilient
T16_3   T16 left    resilient
T16_1   T16 left    susceptible 
T16_2   T16 left    susceptible 
T16_3   T16 left    susceptible 
T16_1   T16 right   control
T16_2   T16 right   control
T16_3   T16 right   control
T16_1   T16 right   resilient
T16_2   T16 right   resilient
T16_3   T16 right   resilient
T16_1   T16 right   susceptible
T16_2   T16 right   susceptible
T16_3   T16 right   susceptible
T24_1   T24 left    control
T24_2   T24 left    control
T24_3   T24 left    control
T24_1   T24 left    resilient
T24_2   T24 left    resilient
T24_3   T24 left    resilient
T24_1   T24 left    susceptible 
T24_2   T24 left    susceptible 
T24_3   T24 left    susceptible 
T24_1   T24 right   control
T24_2   T24 right   control
T24_3   T24 right   control
T24_1   T24 right   resilient
T24_2   T24 right   resilient
T24_3   T24 right   resilient
T24_1   T24 right   susceptible
T24_2   T24 right   susceptible
T24_3   T24 right   susceptible

Answer 1

[Derrik]

see this vignette for DESeq2 time-series experiments

http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#time-course-experiments