Is this the correct DESeq2 design for model with interaction terms and batch effect and paired samples?

Question

[vromman.marieke]

Hello,

I'm looking if someone can confirm or adjust the design for DESeq2 for an experiment with an interaction term (Genotype and Treatment), a batch effect (Differentiation_replicate) and paired samples (DonorID).

Based on the DESeq2 Vignette, these are the three recommended adjustments:

• Interaction term: make a new column with the two columns that interact into 'group' and use design = ~ group
• Batch effect: design = ~ batch + condition
• Paired design: design = ~ subject + condition

Is it correct to combine these recommendation into the following model?

design = ~ batch + subject + group

or in our case

design = ~ Differentiation_replicate + DonorID + Genotype_Treatment

Thanks a lot!

[ATpoint]

Can you post colData(dds)? That will help getting an idea how donors relate to the design here.