Hi,
I am just starting working with DESeq. I have a question regarding the basic biological interpretation of DESeq based DE gene expression. There are two situations I have listed below and I would like to know which one is more biologically relevant
I have two treatment groups: treatment 1 and treatment2 and I am comparing them with a control group all with three replicates. I devised my study as
1. I created a dataframe containing counts of all 9 count files and from this dataframe, I am creating comparisons as: T1 vs Control, T2 vs Control and T2 vs T1.
2. I create a dataframe everytime I create a comparison like when I am comparing T1 vs Control, then I am creating a dataframe with 6 count files. Again when I am comparing T2 vs Control I am creating another dataframe with 6 count files.
I want to know which of these two design strategies will give me a more accurate result as to what effects T1 and T2 are causing when compared with control and how are T1 and T2 different as well as similar?