[R] Multiple comparisons on Anova.mlm object

Kaufman Gabriel gabriel.kaufman at umontreal.ca
Fri Apr 16 21:31:45 CEST 2010

I would like to perform multiple comparisons or post-hoc testing on the independent variable in an Anova.mlm object generated by the Anova function of the car package. I have defined a multivariate linear model and subsequently performed a repeated measures ANOVA as per the instructions in section #3 of the following comprehensive tutorial on the subject from the Gribble lab at UWO: 
Unfortunately, since my data has missing values,I can't seem to use the classical univariate approaches of aov() or lme() (suggested in sections #1 and #2 of the tutorial linked to above).

The relevant portions of the R console output are copied below (redacted somewhat for intellectual property considerations). In sum, I am stuck at the Anova.mlm object, as I cannot seem to apply any of the standard multiple comparisons functions such as pairwise.t.test or p.adjust....

Thank you in advance for your help.

Gabriel Kaufman
Orthopedic Molecular Biology Laboratory
Centre de recherche CHU Sainte-Justine
Montreal, Quebec


R console output

> # define Treatment group as the factor defining the intra-subject model
> as.factor(Treatment)
> ## define repeated measures linear model
> # define repeated-measures data as matrix vector
> RM <- cbind(repeated_measure_1, repeated_measure_2, repeated_measure_3, repeated_measure_4, repeated_measure_5)
> mlm <- lm(RM ~ Treatment, data = RMdata.file)
> # load required package car
> library(car)
> ## Define Anova model object for repeated-measures ANOVA
> # define idata data frame
> idata <- data.frame(RM = factor(1:5))
> # define Anova object
> mlm.aov <- Anova(mlm, idata = idata,idesign = ~RM, type = "II")
> # display class of Anova object
> class(mlm.aov)
[1] "Anova.mlm"
> # display session information
> sessionInfo()
R version 2.10.1 (2009-12-14)

[1] en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base   

other attached packages:
[1] car_1.2-16

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