Is 2-way ANOVA appropriate?

#1
I have 2 groups (Treatment 1 and Treatment 2) with measurements at 5 timepoints through 24 hours. I want to use post tests to compare Treatment 1 and 2 at each timepoint. If the two groups contain completely different subjects is it still appropriate to use a 2-way ANOVA or does it have to be the same subjects that receive Treatment 1 and Treatment 2?
 
#2
You can use a 2-way ANOVA but notice that it is a repeated measures ANOVA. That is, you have one in-between groups variable (Treatment) and one within groups variable. You also should notice that since you will want to use an alpha correction, it is best you have a large sample.
 
#3
Got it thanks. Also, there is a fairly big difference in baseline values between the two treatment groups. To account for this difference is it possible to calculate percent change or delta from baseline at each time point and then make pairwise comparison between treatment 1 and 2 (I’m interested if the magnitude of increase at each time point is different between treatment 1 and 2) or is it absolutely necessary to run ANCOVA with the difference at baseline as the covariate (more difficult with my software)? Any other alternatives?