[BioC] RE: Design/contrast matrix for limma

[Jordi Altirriba Gutiérrez]

Hi Anthony,

Now I'm analysing my data (Affymetrix) and I have also a 2x2 factorial 
design. I think that I could help you, but I have two questions:
1.- What kind of microarrays do you have? Affymetrix, cDNA, ...
2.- How many replicates do you have?
Moreover, if you want to begin to make it yourself, you can see the packages 
LIMMA (there are also the affylmGUI and the limmaGUI developmental packages 
[I think that GUI are clearer], for Affymetrix and cDNAarrays) and 
factDesign. For more information about LIMMA look at: 
http://bioinf.wehi.edu.au/limma/ and their vignettes in the Bioconductor web 
and for more information about factDesign read the vignette enclosed to the 
package (I recommend you to use the developmental version 1.1.2).
I hope that it helps.
Cheers,

Jordi Altirriba - Ph.D. student
IDIBAPS - Hospital Clinic - Barcelona - Spain

>Date: Fri, 30 Apr 2004 14:29:50 +0930
>From: "Chris Wilkinson" <Christopher.Wilkinson at adelaide.edu.au>
>Subject: [BioC] RE: Design/contrast matrix for limma
>To: <bioconductor at stat.math.ethz.ch>
>Message-ID:
>	<PBEHINCJPDMIOIIPFKLOMEGICAAA.Christopher.Wilkinson at adelaide.edu.au>
>Content-Type: text/plain;	charset="US-ASCII"
>
>Hi Anthony,
>
> > How do I set up a design and contrast matrix for the following 
>experiment.
> >
> > I have unstimulated cells and stimulated cells for individuals with
> > and without disease.
> >
> > sample groups
> >
> > 1	Disease		Unstimulated
> > 2	Disease		Stimulated
> > 3	No Disease	Unstimulated
> > 4	No Disease	Stimulated
> >
> > Although I can set up design matrix for all two way comparisons, I am
> > really interested in what genes are different between disease and no
> > disease after stimulation of the cells.
>
>I think what you have is a 2x2 factorial experiment. Check out the weaver
>mutant data example in the limma example. In your case the first factor is
>Disease (no disease & disease) and the second factor is Stimulation(unstim,
>stim). What is of most interest is the interaction of disease and
>stimulation (DxS).
>             Unstimulated   Stimulated
>No Disease  00 ----------- 0S
>             |              |
>             |              |
>    Disease  D0------------ DS
>
>The columns in the design matrix are Disease, Stim and (DiseaseXStim).
>I would also suggest you look over Glonek and Solomon, Factorial and time
>course designs for cDNA microarray experiments. Biostatistics 2004
>Jan;5(1):89-111. (A copy is also available at
>http://mag.maths.adelaide.edu.au/documents.html) It has a very nice
>discussion on factorial designs, in particular 2x2 designs which I think 
>you
>would find helpful.
>
>Cheers
>Chris
>
>Dr Chris Wilkinson
>
>Research Officer (Bioinformatics)        | Visiting Research Fellow
>Child Health Research Institute (CHRI)   | Microarray Analysis Group
>7th floor, Clarence Rieger Building      | Room 121
>Women's and Children's Hospital          | School of Applied Mathematics
>72 King William Rd, North Adelaide, 5006 | The University of Adelaide, 5005
>
>Math's Office (Room 121)        Ph: 8303 3714
>CHRI   Office (CR2 52A)         Ph: 8161 6363
>
>Christopher.Wilkinson at adelaide.edu.au
>
>http://mag.maths.adelaide.edu.au/crwilkinson.html
>

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