The main regression formula I am using is as follows (Both the Group and Time variables are binary):
lmer.fit <- lmerTest::lmer(corrmcc ~ Group * Time + (1|ID),
data = sm.dat)
summary(lmer.fit)
# Fixed effects:
# Estimate Std. Error df t value Pr(>|t|)
# (Intercept) 429.92 36.14 65.74 11.896 <2e-16 ***
# GroupTTNS -37.75 51.64 65.74 -0.731 0.467
# TimeEoS -55.68 34.92 40.36 -1.595 0.119
# GroupTTNS:TimeEoS -23.23 50.47 40.73 -0.460 0.648
As you can see, the Time variable (or TimeEoS) has a p-value of > 0.05. That is, there is no significant difference in the outcome between the two time points.
Then I applied the emmeans function with a bar (|) for a post-hoc analysis as follows:
pairs(emmeans(lmer.fit, ~ Time | Group))
Group = Control:
contrast estimate SE df t.ratio p.value
Baseline - EoS 55.7 35.0 42.0 1.592 0.1189
Group = TTNS:
contrast estimate SE df t.ratio p.value
Baseline - EoS 78.9 36.5 42.7 2.161 0.0364
Here, we can observe that for the TTNS group, the difference between the baseline and EoS is statistically significant (i.e., p-value = 0.0364, < 0.05).
However, when I applied the same function but with an asterisk (*), I obtained an opposite result as follows:
pairs(emmeans(lmer.fit, ~ Time * Group))
contrast estimate SE df t.ratio p.value
**Baseline Control - EoS Control 55.7 35.0 42.0 1.592 0.3940**
Baseline Control - Baseline TTNS 37.8 51.6 66.9 0.731 0.8843
Baseline Control - EoS TTNS 116.7 53.4 71.2 2.184 0.1376
EoS Control - Baseline TTNS -17.9 52.8 69.8 -0.340 0.9864
EoS Control - EoS TTNS 61.0 54.6 73.6 1.118 0.6797
**Baseline TTNS - EoS TTNS 78.9 36.5 42.7 2.161 0.1508**
Here, the difference between the baseline and EoS in the TTNS group is not significant with a p-value of 0.15.
I am sure that I am missing something, but I am having trouble finding what is causing the differences. Any suggestions and comments would be greatly appreciated!