Hallo,

I am new here, so thanks for your help. I need R code to analyze RNA-Seq counts with DESeq2, for dataset that has 4 Genotypes (G) in control and treated conditions (C) each in 3 replicates. I would need all levels plus G*C interactions. If anyone has similar code please share it.

Many thanks, DR

The vignette is usually an awesome code repository for starters: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#interactions

Please explain what is unclear after reading it. Be also sure to read the Initial note: part of the Interaction paragraph, so combining genotype and condition into a single factor which might dealing with interactions quite much easier.