[BioC] contrast matrix in LIMMA

[Jenny Drnevich]

Dear Erika,

Have you read through the limma vignette? 
limmaUsersGuide() . It seems like you have a 
combination of section 7.3 Common Reference 
Designs and 8.2 Technical Replication. Please 
read through these, and if you're still having 
trouble, write back with examples of the design 
and contrast matrices you've tried, and why you 
think they are or are not working.

Good luck,
Jenny

At 03:23 AM 9/15/2008, Erika Melissari wrote:
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>Hello all,
>
>
>by using LIMMA package I'm setting the contrast 
>matrix to discover differentially expressed 
>genes in a dual-color microarray experiment.
>
>In this experiment I observed the expression 
>levels of mRNA samples of three different 
>phenotypes compared to the expression levels of a wild-type sample.
>
>My experimental design is a reference design 
>that is each mRNA sample is hybridized onto the 
>same array with the wild type sample, and a 
>dye-swap for each array is realized.
>
>
>
>Phenotype 1:
>
>
>
>mRNA1.1 (green) à WT (red)
>
>mRNA1.1 (red) à WT (green)
>
>
>
>mRNA1.2 (green) à WT (red)
>
>mRNA1.2 (red) à WT (green)
>
>
>
>And so on
>
>
>
>Phenotype 2:
>
>
>
>mRNA2.1 (green) à WT (red)
>
>mRNA2.1 (red) à WT (green)
>
>
>
>mRNA2.2 (green) à WT (red)
>
>mRNA2.2 (red) à WT (green)
>
>
>
>And so on
>
>
>
>Phenotype 3:
>
>
>
>mRNA3.1 (green) à WT (red)
>
>mRNA3.1 (red) à WT (green)
>
>
>
>mRNA3.2 (green) à WT (red)
>
>mRNA3.2 (red) à WT (green)
>
>
>
>And so on
>
>
>
>I'm interested in determining differentially 
>expressed genes for each phenotype respect to WT 
>sample that is "Phenotype 1" àWT, "Phenotype 2" àWT, "Phenotype 3" àWT.
>
>Moreover, I'm interested in determining   the 
>differentially expressed genes in commom between 
>each couple of phenotypes that is"Phenotype 1" 
>à"Phenotype 2", "Phenotype 1" à"Phenotype 3", "Phenotype 2" à"Phenotype 3".
>
>Does anyone know how I can set the contrast 
>matrix to be inserted in lmFit function?
>
>What is the model to be used?
>
>
>Thank you for your help
>
>Erika
>
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>
>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at illinois.edu