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jg295@mole.bio.cam.ac.uk jg295 at mole.bio.cam.ac.uk
Wed Dec 14 16:12:20 CET 2005

Hi there, I'm trying to analyze the data of 8 dual-color microarray 
hybridizations, but I' a bit stuck with the design matrix. I tried looking 
into the previous emails from the list but could not quite find the answer. 
It'd be great if you could help out. The experimental design is fairly 
straightforward in priciple: this is a time course with only two time 
points. For each time point I have duplicate samples and dye swaps for each 
sample. Something like this below:

1        Wt1     Mu1     Time point 1
2        Mu1     Wt1     Time point 1
3        Wt1     Mu1     Time point 2
4        Mu1     Wt1     Time point 2
5        Wt2     Mu2     Time point 1
6        Mu2     Wt2     Time point 1
7        Wt2     Mu2     Time point 2
8        Mu2     Wt2     Time point 2

Apart from the time effect, I would actually like to test if the 
"replicates" are actual replicates, since the biological data seem to 
indicate they are not quite so similar. If I assume that the replicates are 
actual replicates, how would the design matrix look like? and if I want to 
see if the replicates are behaving differently, do I have to design two 
different matrices and analyse each set of data independently? Sorry if the 
questions are too naive!

Thanks in advance

Jose Garcia-Bernardo
University of Cambridge
Downing Street CB2 3DY
Cambridge UK

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