In DESeq2, you can set up a multi-factor design like:
This would give you the differences attributable to the "treatment" while accounting for the "celltype".
However, what if you are interested in the differences in response to treatment in different cell types? Instead of looking for the effects of treatment regardless of cell type, you want the effects of treatments that are unique to a specific cell type. How would you get those?
Code:
design(dds) <- formula(~ celltype + treatment)
However, what if you are interested in the differences in response to treatment in different cell types? Instead of looking for the effects of treatment regardless of cell type, you want the effects of treatments that are unique to a specific cell type. How would you get those?
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