# Tukey HSD following lme

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## Tukey HSD following lme

 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 [hidden email] ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.