# [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:
http://gribblelab.org/2009/03/09/repeated-measures-anova-using-r
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....

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)
i386-apple-darwin9.8.0

locale:
[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

```