[BioC] (no subject)

[Kort, Eric]

The package limma will allow you to address these issues.  What's more, its user's guide is a wonderful overview of the analysis of microarray data accessible to non-mathematicians (like me).  You can obtain the user's guide by installing the package, or directly here (for example):

http://cmmg.biosci.wayne.edu/Education/mbg8680/limma_users_guide.pdf

I hope that this journey leads you to the conclusion that your replicates are replicates, otherwise it's back to the laboratory as it is difficult to perform statistical analysis with N=1.

Enjoy,

Eric


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch on behalf of jg295 at mole.bio.cam.ac.uk
Sent: Wed 12/14/2005 10:12 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] (no subject)
 
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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