[BioC] VennDiagram quesiont in limma

[Gordon Smyth]

Dear Jianping,

I may be mis-interpreting your question (I'm not sure what you mean 
by a "session"), but I think you just want the gene lists 
corresponding to the counts in the Venn diagram.

Suppose you have a fitted model 'fit' with columns "A", "B" and "C". Then

   vennDiagram(fit)

will give you a Venn diagram with 8 counts in it. You can do the 
diagram in two steps

   results <- decideTests(fit)
   vennDiagram(results)

and this allows you to extract the gene lists. Suppose you want the 
genes DE for both "A" and "B", you could use

   myGenes <- apply(results[,c("A","B")],1,all)
   fit$genes[myGenes,]

to see the gene list.

Best wishes
Gordon

>Date: Tue, 30 May 2006 13:22:08 -0400
>From: Jianping Jin <jjin at email.unc.edu>
>Subject: [BioC] VennDiagram quesiont in limma
>To: BioConductor_list <bioconductor at stat.math.ethz.ch>
>Message-ID: <DBCD9D517C98493F3A37FA9D at unc-jpjin.pmbb.med.unc.edu>
>Content-Type: text/plain; charset=us-ascii; format=flowed
>
>Dear list:
>
>I am wondering if there is an easy way or a function by which one can
>extract (list) any session of genes, either in common or not in common with
>other sesseion(s), in vennDiagram of limma? I assumed that vennDiagram
>should be able to allow to do that. But I did not find anything like that
>after reading the on-line instructions.
>
>Many thanks if you could help me out!
>
>Jianping
>
>xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>x Jianping Jin Ph.D.            x
>x Bioinformatics scientist      x
>x Center for bioinformatics     x
>x 3133 Bioinformatics Building  x
>x CB# 7104                      x
>x University of North Carolina  x
>x Chapel Hill, NC 27599         x
>x Tel: (919)843-6105            x
>x Fax: (919)843-3103            x
>x E-mail: jjin at email.unc.edu    x
>xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx