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 Schädel > Institute of Botany > University of Basel > Schönbeinstrasse 6 > CH-4056 Basel > ph. +41 61 267 35 06 > fax +41 61 267 29 80 > E-Mail [EMAIL PROTECTED] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > -- View this message in context: http://www.nabble.com/Tukey-HSD-following-lme-tp20560069p20561633.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
