[BioC] venn diagram

James W. MacDonald jmacdon at med.umich.edu
Thu Jul 30 17:24:10 CEST 2009

Stephen V. Su wrote:
> 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 ....

It depends on what you want when you say 'extract out the genes'. If 
perhaps you want to have annotated tables for each quadrant, then look 
at the vennSelect function in the affycoretools package. This will 
output either HTML or text tables that can be opened using a browser or 
spreadsheet program, respectively.



> Your help is greatly appreciated and I thank-you in advance of your
> considerations
> Steve
> [[alternative HTML version deleted]]
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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618

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