Deseq2 interaction terms

[denalitastic]

Hello, I have been trying to figure out how to deal with combining interaction terms in Deseq2. I have pored over all posts and the tutorials including the manual.

My design is as follows design = ~cell + drug + time + drug:time

Drug: V,L,T
Time: 0,1,2,6,12,24,48
cell: A ,B

I am interested in the difference of differences. Basically I am looking for what genes are regulated differently between 2 treatments or between 1 treatment vs the other 2. And i am pooling some time points. So for example for drug T i have the condition effect of early vs late (early being time points 1 and 6 combined) and late being (24 and 48 combined). And how does this compare to the case of drug L. All this while controlling for cell type. My solution is using the design above. Assume here that I have made L drug my reference.

this is from resultsNames

 [1] "Intercept"          "cell_A_vs_B" "drug_V_vs_L"     "drug_T_vs_L"   
 [5] "time_1_vs_0"        "time_6_vs_0"        "time_12_vs_0"       "time_24_vs_0"      
 [9] "time_48_vs_0"       "drugV.time1"      "drugT.time1"     "drugV.time6"     
[13] "drugT.time6"     "drugV.time12"     "drugT.time12"    "drugV.time24"    
[17] "drugT.time24"    "drugV.time48"     "drugT.time48"

late vs early condition , T drug vs L drug (L is reference level)

contrast = list(c("drugT.time48", "drugT.time24"), c("drugT.time1","drugT.time6")), listValues = c(0.5,-0.5)

For 48hrs vs early for V vs L (L is reference)

contrast = list(c("drugV.time48"), c("drugV.time1","drugV.time6")), listValues = c(1,-0.5)

What if i wanted condition effect of Late vs Early and the difference and T & V combined vs L? My guess is this. (where L is reference)

c("drugT.time48", "drugT.time24", "drugV.time48", "drugV.time24"), c("drugT.time1", "drugT.time6", "drugV.time1", "drugV.time6"), listValues = c(0.25,-0.25)

Is this correct? Are there other methods of doing this. What if I made V my reference and asked the same questions. This seems more complicating but it might help explicate the DESeq syntax. I can add anything to this post that is necessary.

Thanks for any help you can provide!