To whom this may concern:

    I must first apologize for not being a bioinformaticist and really only "pretend" to know how to use R to analyze microarray.  But i do understand the concepts of Limma and when to apply it.  I think it is a really powerful way to analyze matrix data.  So, if you don't mind, I would like to ask you a question regarding Venn Diagrams.  I have generated a RMA-processed expression set for 3 different conditions (each condition has a minimum of 8 CEL files- Affy 0.5 genome rat chip), fed it through limma to create a statistical computation of all the genes that are differentially expressed and created a venn Diagram to depict the results.  A general input functions of what i just wrote is depicted here:


> fit <- lmFit(x, design)
 
> cont.matrix <- makeContrasts(x3Dvsinvivo = x3D - invivo,
+ x3Dvsx2D = x3D - x2D,
+ x2Dvsinvivo = x2D - invivo, levels = design)
> fit2 <- contrasts.fit(fit, cont.matrix)
> fit2 <- eBayes(fit2)
> results <- decideTests(fit2)
> vennDiagram(results)
 
My question is:  How do I extract out the genes that reside in each of the quadrant in the Venn diagram?  Is there a way for me to say, retrieve the 108 genes that are unique to condition A, 98 genes unique to condition B and C, and so on ....
 
Your help is greatly appreciated and I thank-you in advance of your considerations
 
Steve


      
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