I am trying to use the DESeq2 package on my count data from a targeted RNA sequencing project. I have a two factor design and was wondering about the correct way how to formulate the design formula.

My `colData(dds)`

looks something like this:

ELS Cort sizeFactor <factor> <factor> <numeric> 101 Co naive 0.9500628 103 Co naive 1.0928817 105 Co naive 1.0856740 107 MS naive 1.1095217 109 MS naive 0.9790554 91 MS naive 1.1911926 93 MS inject 0.9647519 95 MS inject 1.1422150 97 Co inject 1.1553050 99 Co inject 1.0367721

and

design(dds)= ~Cort * ELS

I now want to analyze the main effects of each factor as well as the interaction effect (comparable to a two-way ANOVA).

With this design I get

resultsNames(dds) [1] "Intercept" "Cort_inject_vs_naive" "ELS_MS_vs_Co" "Cortinject.ELSMS"

Do I get the main `Cort `

effect with this results formula?

results(dds, name = “Cort_inject_vs_naive”)

How is the `ELS `

factor handled in this case? Is the `Cort `

effect corrected for `ELS `

or is only a subset of the data with `ELS=Co`

used?

Thanks a lot for your help!