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Interactions in DESeq2

I am running RNA Sequencing Data in DESeq2 and my model is design= Pubertal.Class * Treatment where my

Pubertal.Classes = Typical(ref), Early, NC, SSS, SSD 
Treatment = Non-Stimulated(ref), Stimulated 


resultsNames(dds)
[1] "Intercept"                                     "Pubertal.Class_Early_vs_Typical"              
[3] "Pubertal.Class_Non.Cycling_vs_Typical"         "condition_Stimulated_vs_Control"              
[5] "Pubertal.ClassEarly.conditionStimulated"       "Pubertal.ClassNon.Cycling.conditionStimulated"

If I want to compare Early-Stimulated vs. Early-Non-Stimulated is the following the correct code?

res.stim_early <- results(dds, contrast = list(c("condition_Stimulated_vs_Control",
                                       "Pubertal.ClassEarly.conditionStimulated")))
deseq2
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updated by swbarnes2 swbarnes2 • written by brooke.bell1299 • brooke.bell1299

1 answer

The more readable way to do compare one subset of samples to another subset of samples is to make a new column that is Pubertal.classes_Treatment and then contrast the two classifications you want to compare to each other.

The interaction design is useful if you want to know what genes respond differently to treatment when you change the class. A 4 group comparison, essentially. But for simple 2 group comparisons, do it the simpler way.

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written by swbarnes2 swbarnes2

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