DESeq2 design for differential expression- 2 groups, 4 time points

Question

[dani.tom]

Hi everyone, I am currently using DESeq2 in R for performing differential expression analysis on a dataset consisting of 2 conditions (control+treatment) and 4 time points, and there are 3 biological replicates for each condition-timepoint.

So the sample data is as in the attached samp.data image

I would like to find all the genes differentially expressed between time points 1,2 and 3 when compared to time point 0. I want to find all the genes in each condition separately (so all the genes changing in the control and all those changing in the treatment).

What would be the correct design for this? Thanks a lot for your help!

Daniella

Answer 1

[rpolicastro]

You want to find both the DEGs that differ in time independent of your conditions, and the DEGs that differ in your conditions independent of time? Are you also interested in genes that differ by conditions and time?

[dani.tom]

Thanks for your response. I'll clarify :)

I'm interested in two results:

1. The DEGs that change in the control condition between time points 1,2 and 3 as compared to time point 0 (so that's 3 comparisons- control 1 vs. 0, control 2 vs. 0, control 3 vs. 0.

2. The DEGs that change in the treatment condition between time points 1,2 and 3 as compared to time point 0 (so that's 3 comparisons- treatment 1 vs. 0, treatment 2 vs. 0, treatment 3 vs. 0.

The sample data for some reason is not shown here, but it is in this link: https://ibb.co/Pc1P83j

[rpolicastro]

In that case the easiest thing to do is to concatenate your time point and type column into one factor column, so you can use contrasts such as control_0 vs control_1.