[R-sig-eco] marginal vs sequential results of lme

[Iannone, Basil]

Dear R users,

I am having a problem with interpreting "anova" results of a linear mixed
effects model.

The data I am analyzing is from study that was set up as a randomized
block design with two factors at two levels. The model is:

       m1 <- lme(Y~A*B, random = ~1|Block)

The design is completely balanced and no data are missing. When I run a
sequential anova I get a p-value = 0.02 for factor B. When I run a
marginal anova (specified by "type = "marginal""), I get a p-value = 0.29
for factor B. The model summary ("summary (m1)" ) agrees with the marginal
test and shows a p-value = 0.29 for factor B. Further when I graph values
of Y against levels of B, I see no difference.

I thought that sequential and marginal anovas should produce the same
results when the design is balanced. Can someone please explain to me why
the results of the "anova(m1)" differ from the results of "anova(m1, type
= "marginal")" and "summary(m1)."

Thanks for your help,


-- 
Basil Iannone
University of Illinois at Chicago
Department of Biological Sciences (MC 066)
845 W. Taylor St.
Chicago, IL  60607-7060
Email: bianno2 at uic.edu
Phone: 312-355-3231
Fax: 312-413-2435
http://www2.uic.edu/~bianno2