Differential Gene expression analysis with two factors

Question

[mahnazkiani]

Hi,

I have a question about RNA-seq data analysis, I have two genotypes and 3 sampling from a different part of the plant in each genotype. I want to analyze both genotypes together using factor analysis with a genotype: stage interaction term. How I can do that? Can I use edgeR?

Appreciate your help, Mahnaz

[mahnazkiani]

Just wondering that does it makes sense to get DEGs from two genotypes and then use venn diagram to find similar DEGs in two genotypes and go through functional analysis after that?

[Devon Ryan]

That would be undesirable when there are known better methods.

Answer 1

[Devon Ryan]

Yes, you can certainly do that with edgeR (or DESeq2 or limma). If you really want the interaction term then use a model of ~genotype*stage and get the adjusted p-values/fold-changes for the interaction. Have a look at section 3.3 in the edgeR user guide for designs including interactions.