Hello List

I have been asked to analyse some data for a colleague. The design consists of a two sets of animals 


First set of three - one leg is treated and the other is not under two different conditions (control & overload are the same animals - control leg is control (!) for treated leg; 


Second set of three - one leg is treated and the other is not under two different conditions (high_fat and high_fat_overload are the same animals with high_fat being control leg for high_fat_overload).

Ideally I'd like to find differences between the treatments.

bip <- structure(list(group = structure(c(1L, 1L, 1L, 2L, 2L, 2L, 3L, 
3L, 3L, 4L, 4L, 4L), .Label = c("control", "overload", "high_fat", 
"high_fat_overload"), class = "factor"), variable = structure(c(1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = "BiP", class = "factor"), 
    animal = structure(c(1L, 3L, 5L, 1L, 3L, 5L, 2L, 4L, 6L, 
    2L, 4L, 6L), .Label = c("rat1_c", "rat1_hf", "rat2_c", "rat2_hf", 
    "rat3_c", "rat3_hf"), class = "factor"), value = c(404979.65625, 
    783511.8125, 677277.625, 1576900.375, 1460101.875, 1591022, 
    581313.75, 992724.1875, 1106941.5, 996600.375, 1101696.5, 
    1171004.375)), .Names = c("group", "variable", "animal", 
"value"), row.names = c(NA, 12L), class = "data.frame")

I chose to analyse this as a mixed effects model with treatment as a fixed effect and animal as random.

library(lme4)
model1 <- lmer(value~group + (1|animal), data=bip)
summary(model1)

And then compare this to no treatment with:

anova(model1)

>From this I wanted to work out whether 'treatment' was significantly affecting BiP levels by calculating the critical value of F for this design. I have 2 groups of animals and 3 animals per group. My calculation for the degrees of freedom for treatment is 4-1=3.

I'm not sure about the degrees of freedom for the denominator though. Since I'm comparing a model with treatment to one without (i.e. the grand mean) would the df for my denominator be 6-1=5?

So I'd then have:

qf(0.95,3,5)

for my critical F value?

Best

iain

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