My dataset is a biological analysis of a disease which takes 3 months to develop, and we're looking at treatment of that disease. The data is gene expression data and we want to identify changes in gene expression over time. This resembles a 2x2 design in which I have equal sized groups as:
trtmnt no-trtmnt 1 month 10 10 3 month 10 10
After thinking about it, I'm not sure if this is really valid for a 2-way ANOVA. The disease develops over the period of 3 months, so the 1 month subjects should look the same regardless of treatment. There are multiple ways to look at this:
1) I could compare trtmnt and no-trtmnt at the 3-month stage. Simple two-group analysis. 2) I could look at 1 month vs 3 month for trtmnt, and then 1 month vs 3 month for no-trtmnt. This would be 2, two-group analyses. But then I would have to compare the two different analyses to look for gene change in common or different. This is where it starts to resemble a 2-way ANOVA, but not really.
I appreciate any thoughts.
EDIT: I should have pointed out that these are animal studies, so we have 10 animals in each group. Rather than taking samples from each animal twice - once at 1 month and once at 3 months - we have 4 different groups, all of which were used for sampling. I hope that makes sense.