[BioC] Timeseries loop design analysis using Limma or Maanova?

[Pete]

Hello all,

I have been asked to analyse a set of timecourse data with an unusual
incomplete loop design. This is the design of this type I have looked at
and I'm not entirely sure how to treat it.

The initial (and fairly easy) question asked of the data is, what are the
differences between the mutant and the control animals at each timepoint?

The second question is how the mutant changes across the timeseries. The
authors
wish to use a bayesian timeseries clustering algorithmn to analyse this, but
this requires a standardised measure for the mutant at each timepoint.

I am unsure quite how to achieve this second point and welcome any
suggestions or references that may help. Is this something I could do in 
Limma or MAanova?


The data are from spotted, two-colour, oligo arrays. There are 6 timepoints.
At each timepoint, tissue samples from 3 individual mutant animals are
compared to a control pool of WT animals at the same timepoint, with dye
swaps. In addition each control pool has then been compared in a dye swap to
the next timepoint control pool. See diagram below (if it comes out
correctly!) or the table further below where a1 a2 a3 represent any 3 
individual animals.



a1t1    a2t1    a3t1           a1t2    a2t2    a3t2      etc............
    \\        ||        //                \\        ||        //
     Control t1  ========= Control t2    ==== etc...............

or

SLIDE        CY3            CY5
1                a1t1            control t1
2                control t1    a1t1
3                a2t1            control t1
4                control t1     a2t1
5                a3t1            control t1
6                control t1    a3t1
7                a1t2            control t2
8                control t2    a1t2
9                a2t2            control t2
10                control t2        a2t2
11                a3t2                control t2
12                control t2        a3t2
13                a1t3                control t3
14                control t3        a1t3
15                a2t3                control t3
16                control t3        a2t3
17                a3t3                control t3
18                control t3        a3t3
19                a1t4                control t4
20                control t4        a1t4
21                a2t4                control t4
22                control t4        a2t4
23                a3t4                control t4
24                control t4        a3t4
25                a1t5                control t5
26                control t5        a1t5
27                a2t5                control t5
28                control t5        a2t5
29                a3t5                control t5
30                control t5        a3t5
31                a1t6                control t6
32                control t6        a1t6
33                a2t6                control t6
34                control t6        a2t6
35                a3t6                control t6
36                control t6        a3t6
37                control t1        control t2
38                control t2        control t1
39                control t2        control t3
40                control t3        control t2
41                control t3        control t4
42                control t4        control t3
43                control t4        control t5
44                control t5        control t4
45                control t5        control t6
46                control t6        control t5


Many thanks

Pete