I am not sure I am building the proper design formula for the question I want to answer
I have the following samples with three factors; clone, the structure and the condition.
clone structure diabetic 1 07 2D Dia 2 21 2D Ctrl 3 23 2D Dia 4 32 2D Ctrl 5 34 2D Dia 6 43 2D Ctrl 7 07 3D Dia 8 21 3D Ctrl 9 23 3D Dia 10 32 3D Ctrl 11 34 3D Dia 12 43 3D Ctrl
I want to pull the differentially expressed genes for structure (2D vs 3D) blocking by clone, and the one differentially expressed by condition (regardless of the structure variable).
I am not sure how to build the design in one call, therefore I have produced the first object to pull 2D vs 3D blocking by clone using the following.
des_structure <- DESeqDataSetFromHTSeqCount(sampleTable = samples, directory = "../data/htseq_geneCounts/", design= ~ clone+structure)
for the condition controlled by structure I have used
des_condidtion <- ddsHTSeq_diabetic <- DESeqDataSetFromHTSeqCount(sampleTable = samples, directory = "../data/htseq_geneCounts/", design= ~ structure+diabetic)
I am not sure whether this is the best way to build the designs.