[R] Repeated measures lme or anova

John Coulthard bahhab at hotmail.com
Fri Jul 4 15:24:34 CEST 2008


Hi

As I can't find an example of my data structure I'd like some advice on which is the most appropriate test for significant effects.  If I should be using either lme or anova, is the relevant example below the best/correct way to do the test?

The Data...
2 groups of patients (5 in GroupA, 7 in GroupB)
3 short acting drugs, (I'm not concerned with residual effects from the previous test effecting the current test)
Each patient is given all 8 possible combinations of the 3 drugs (8 measurements from each subject = repeated measures)
The dependent effects are metabolite levels in the blood, a continuous variable but often skewed towards 0.1 which is the minimum detectable level.
I'm look for individual and combined effects of Group and Drug.
There are ~400 metabolites which I intend to test independently. (I know that will leave me with a multiple testing issue)

What I've worked out for lme is
> summary(test.lme <- lme(Value ~ Group*Drug1*Drug2*Drug3 - 1, test,random = ~1|Patient))
> anova(test.lme)


and for anova is
> summary(aov(Value~(Group*Drug1*Drug2*Drug3)+Error(Patient/(Drug1*Drug2*Drug3)),test))

The full structure of the 'test' data table for one metabolite is below.

Thanks for your time and any thoughts you may have.
Ann

> test
   Patient Group Drug1 Drug2 Drug3  Value
1        1     A     0     0     0 446.70
2        1     A     0     0     1   0.10
3        1     A     0     1     1   0.10
4        1     A     0     1     0 328.20
5        1     A     1     0     0   0.10
6        1     A     1     0     1   0.10
7        1     A     1     1     1   0.10
8        1     A     1     1     0   0.10
9        2     B     0     0     0   0.10
10       2     B     0     0     1  69.93
11       2     B     0     1     0 878.30
12       2     B     0     1     1   0.10
13       2     B     1     0     1   0.10
14       2     B     1     0     0   0.10
15       2     B     1     1     1   0.10
16       2     B     1     1     0   0.10
17       3     A     0     0     0   0.10
18       3     A     0     0     1   0.10
19       3     A     0     1     0   0.10
20       3     A     0     1     1   0.10
21       3     A     1     0     1   0.10
22       3     A     1     0     0   0.10
23       3     A     1     1     0   0.10
24       3     A     1     1     1   0.10
25       4     B     0     0     1   0.10
26       4     B     0     0     0 688.50
27       4     B     0     1     0 541.00
28       4     B     0     1     1   0.10
29       4     B     1     0     0   0.10
30       4     B     1     0     1   0.10
31       4     B     1     1     1   0.10
32       4     B     1     1     0   0.10
33       5     B     0     0     0   0.10
34       5     B     0     0     1   0.10
35       5     B     0     1     0 541.60
36       5     B     0     1     1   0.10
37       5     B     1     0     0   0.10
38       5     B     1     0     1   0.10
39       5     B     1     1     0   0.10
40       5     B     1     1     1   0.10
41       6     B     0     0     1  58.29
42       6     B     0     0     0 353.60
43       6     B     0     1     0 523.30
44       6     B     0     1     1   0.10
45       6     B     1     0     0   0.10
46       6     B     1     0     1   0.10
47       6     B     1     1     0   0.10
48       6     B     1     1     1   0.10
49       7     A     0     0     0 351.03
50       7     A     0     0     1   0.10
51       7     A     0     1     1   0.10
52       7     A     0     1     0   0.10
53       7     A     1     0     0   0.10
54       7     A     1     0     1   0.10
55       7     A     1     1     1   0.10
56       7     A     1     1     0   0.10
57       8     A     0     0     0 299.80
58       8     A     0     0     1   0.10
59       8     A     0     1     0   0.10
60       8     A     0     1     1   0.10
61       8     A     1     0     1   0.10
62       8     A     1     0     0   0.10
63       8     A     1     1     0   0.10
64       8     A     1     1     1   0.10
65       9     B     0     0     0 355.50
66       9     B     0     0     1   0.10
67       9     B     0     1     0 737.90
68       9     B     0     1     1 322.60
69       9     B     1     0     0   0.10
70       9     B     1     0     1   0.10
71       9     B     1     1     0   0.10
72       9     B     1     1     1   0.10
73      10     A     0     0     1 462.90
74      10     A     0     0     0 657.50
75      10     A     0     1     0  82.13
76      10     A     0     1     1   0.10
77      10     A     1     0     1   0.10
78      10     A     1     0     0   0.10
79      10     A     1     1     1   0.10
80      10     A     1     1     0   0.10
81      11     B     0     0     0 386.70
82      11     B     0     0     1 279.40
83      11     B     0     1     1 407.30
84      11     B     0     1     0 485.20
85      11     B     1     0     1   0.10
86      11     B     1     0     0   0.10
87      11     B     1     1     0   0.10
88      11     B     1     1     1   0.10
89      12     B     0     0     1   0.10
90      12     B     0     0     0 705.10
91      12     B     0     1     0 706.20
92      12     B     0     1     1 450.20
93      12     B     1     0     1   0.10
94      12     B     1     0     0   0.10
95      12     B     1     1     0   0.10
96      12     B     1     1     1   0.10
> 

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