I am comparing fluorescence levels in baseline condition, after a pretreatment, and after a treatment with a drug. The statistical software I am using is GraphPad prism.
Using a paired t-test, I have detected a significant difference (p = 0.0382), between my pretreatment group and my treatment group. There is also a highly significant difference between the baseline condition and the pretreatment (p = 0.0001), using a paired t-test, but I am not so interested in this as this effect is well established.
Now as I have three groups, I initially used a repeated measures ANOVA. The ANOVA is highly significant (p <0.0001), which was to be expected due to the large difference between the baseline and pretreatment group. However, the a post-hoc tukey test does not become significant for the pretreatment vs treatment groups, even at P<0.1. So now I am wondering whether it would be justified to indicate a significant difference between the pretreatment and treatment group, given that a t-test is singnificant, but this is not the most appropriate test. Can indicate significance based on the t-test, or do I have to rely on the ANOVA? And what explains the difference between the two?