[BioC] VennDiagram quesiont in limma

jjin at email.unc.edu jjin at email.unc.edu
Thu Jun 1 16:23:03 CEST 2006

Hi Gordon,

Thanks very much for your help! That is what I wanted to extract. But 
what if I wanted genes DE for "A" and "B" but "C"? Or just for "A", not 
"B" and "C"?

best wishes!


Quoting Gordon Smyth <smyth at wehi.EDU.AU>:

> 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
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>> x Jianping Jin Ph.D.            x
>> x Bioinformatics scientist      x
>> x Center for bioinformatics     x
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