I kept my samples at different temperatures (4 c &25 c) --> the first factor. for 6 months and took samples at different time points(0,2,5,6 months)--> 2nd variable at each time point I stress at 50 oC so I have stressed and nonstressed --> 3rd variable to see what are the genes important for stress resistance there is another factor which is the batch effect(A&B).

what is the best model to use to answer the questions:- 1- genes up presented at later time points. vs early one at these 2 different temperature 25&4. 2- what are the genes increased/decreased with stress at different time points and different storage temperature. is the following formula is the right one?

dds <- DESeqDataSetFromMatrix(countData=counts.dffh, colData=seq, design = ~ batch+Temp+Time+Treatment:Time+Time:Temp)