Hi,

I was just wondering if it okay to use mixed model in DE analysis with deseq2. If yes, in what circumstances. For example, I have multiple tissue samples collected from the same individual where my variable of interest is a disease. I have multiple categorical variable associated with the samples such as age, sex, RIN, PMI. Which model will be more appropriate,

formula = ~ age + sex + RIN + PMI + tissue + disease 

or

formula = ~ (1| individual) + RIN + PMI + disease

Thanks in advance.

Nurun

We don't have the ability to use any random effects in the design. Here are some posts on the topic:

https://www.google.com/search?q=site:support.bioconductor.org+deseq2+random+effects