Dear all,

I'm involved in several projects where RNAseq data are collected in time at multiple time points on the same mouse or patient and the goal is to detect DE genes over time or at specific time points. I have checked the DESeq2 vignette (section: Time-series experiments) but it is not clear to me how exactly DESeq2 models the correlation between the repeated measurements collected on the same unit. Could you please refer me to the right documentation to read about it?

Thank you in advance for your help.

Kind regards,
Roula

Roula

Have a look at the time series example in the RNA-seq workflow. There have been several threads on time courses in this forum, I encourage you to search the forum for relevant threads. E.g., A: DESeq2 time series

You could also opt to provide more detail on your experimental design, biological question and the model formula(e) and test contrasts you intend to use, in case someone has a more specific answer. To read more on underlying statistical theory, please refer to textbooks on (generalized) linear models and ANOVA. DESeq2 uses the standard formula language of R for this.

Hope this helps

Wolfgang