I am learning DESeq2 and have a question of setting up design matrix for my experiment,

I have 3 cells lines and each were treated with either drug or placebo, and the whole experiment was repeated 3 times. There are large variability among cell lines and even bigger than the drug effects. However,  I am just interested in a comparison of drug vs placebo and consider cell lines are biological replicates. In this case, do I still need to put cells as a variable in the design as shown below? Thanks in advance.

design = ~ cell + treatment 

design = ~ treatment

Tom

You should put cell in the design, this is exactly the same as the example in our workflow:

https://bioconductor.org/packages/3.7/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#the-deseqdataset-object-sample-information-and-the-design-formula