Hi Christina,
>> How can this happen? How can the p-values from the Tukey become
>> significant when the lme-model wasn't?
The link below, with an explanation by Prof. Fox is relevant to your
question:
http://www.nabble.com/Strange-results-with-anova.glm()-td13471998.html#a13475563
Another way to see the error of your ways is to fit your model using the
default treatment contrasts and then do a Dunnett post hoc using glht:
##
summary(glht(hc, linfct=mcp(CO2="Dunnett")))
Regards, Mark.
C.Schaedel wrote:>
> Hi everyone
>
> I'm using Tukey HSD as post-hoc test following a lme analysis. I'm
> measuring hemicelluloses in different species treated with three
> different CO2 concentrations (l=low, m=medium, h=high). The whole
> experiment is a split-plot design and the Tukey-function from the
> package multcomp is suitable for lme-analysis with random factors.
>
> The analysis works fine but I get a non significant lme-result and if I
> do a Tukey afterwards (I know that one usually does a Tukey following a
> significant anova-result) I get highly significant p-values for two
> multiple comparisons.
>
> How can this happen? How can the p-values from the Tukey become
> significant when the lme-model wasn't?
>
>
> the data are: d
>
> Species Block CO2 hemicell
> Ps a l 9.027363
> Ps b l 9.647537
> Ps a m 10.051916
> Ps b m 10.112294
> Ps a h 10.342162
> Ps b h 10.303091
>
>
> my lme model:
> anova(hc<-lme(asin(sqrt(0.01*hemicell))~CO2,random=~1|Block/CO2,data=d))
>
> numDF denDF F-value p-value
> (Intercept) 1 2 30403.248 <.0001
> CO2 2 2 8.051 0.1105
>
>
> Tukey with the lme-object:
>
> summary(glht(hc, linfct=mcp(CO2="Tukey")))
>
> yielding:
>
> Linear Hypotheses:
> Estimate Std. Error z value p value
> m - l == 0 0.012616 0.004317 2.922 0.00963 **
> h - l == 0 0.016590 0.004317 3.843 < 0.001 ***
> h - m == 0 0.003973 0.004317 0.920 0.62738
> ---
> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05
'.' 0.1 ' ' 1
> (Adjusted p values reported -- single-step method)
>
>
> Thank you very much for your help
>
> Christina
>
>
>
> --
> Christina Sch?del
> Institute of Botany
> University of Basel
> Sch?nbeinstrasse 6
> CH-4056 Basel
> ph. +41 61 267 35 06
> fax +41 61 267 29 80
> E-Mail C.Schaedel at unibas.ch
>
> ______________________________________________
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
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