[R-sig-ME] p-values from model fitting or glht?
Cristiano Alessandro
cri@@le@@@ndro @ending from gm@il@com
Wed Jun 6 23:30:13 CEST 2018
Hi all,
I am running a mixed model to compare two groups. This is repeated measure
design. The model is very simple:
linM11 <- lme(values ~ grf, random = ~1|id, data=dat_trf,
na.action=na.omit, method = "ML", control=lCtr )
where grf is a factor with two levels. I am asking if the two levels are
significantly different. When I call summary() I obtain (among the other
things):
> summary(linM11)
Fixed effects: values ~ grf
Value Std.Error DF t-value p-value
(Intercept) -8.513064 0.9908567 16 -8.59162 0.0000
grf1 3.027705 1.4158346 15 2.13846 0.0493
which makes me think that the two groups are barely significantly
different. But If I run this post-hoc test I get this other (quite
different) result:
> ph_conditional <- c("grf1 = 0");
> linM.ph <- glht(linM, linfct = ph_conditional);
> summary(linM.ph)
Linear Hypotheses:
Estimate Std. Error z value Pr(>|z|)
grf1 == 0 3.028 1.372 2.206 0.0274 *
Which one should I trust? I am always confused on whether I should use the
p-values of the model fit or those of the post-hoc tests. If I had multiple
tests, I would certainly run the post-hoc and adjust for multiple
comparisons (with glht). But here there is only one test, and I am not sure
why I get so different results, and which one I should trust.
Thanks
Cristiano
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