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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