[BioC] Timeseries loop design analysis using Limma or Maanova?
Pete
p.underhill at har.mrc.ac.uk
Mon Feb 13 17:07:04 CET 2006
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
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