I am recently analyzing RNAseq data with multiple factors: 2 cell types (A, B), 6 time points (t1, t2, t3, t4, t5, t6), 4 drug concentrations (c1,c2,c3,c4). Normally what I did for one factor RNAseq is to compare TREATMENT to CONTROL and get a list of DE genes. But in this case, I will do so many different combinations:
For example, I can compare the drug treatment effect difference on different cell types: A-t1-c1 compare with B-t1-c1, A-t1-c2 compare with B-t1-c2, A-t1-c3 compare with B-t1-c3, A-t1-c4 compare with B-t1-c4, A-t2-c1 compare with B-t2-c1....etc.
I can also compare the treatment of the drug in different time point, for example. There will different combination and difficult to find the key factor.
I think it won't be too difficult to develop one program that take the data frame structure which contain all the factor information and analysis the DE genes in one go. But I searched and have not found any. Does anyone aware of this kind of program? Thanks.