[BioC] Venn Diagrams in Limma

Gordon Smyth smyth at wehi.edu.au
Tue Oct 28 02:56:17 MET 2003

At 04:14 AM 28/10/2003, Jason Skelton wrote:
>I have a couple of questions about the venn diagrams options in Limma
>Once you have obtained your venn diagram how can you "identify" or make 
>lists of genes from the different venn components ?

Venn diagrams are by their nature simply overall counts. But you can easily 
identify the relevant genes from the 'classification' object from which the 
Venn diagram is computed.

>I'd also like to be able to use the false discovery rate option that can 
>beused in classifyTestsP method for my venn diagram but I also want to use 
>data that I've received from makeContrasts and contrast.fit which I can 
>only use in classifyTests but I can't use "fdr" in that function....
>Is there a particular reason why I can't do this ?

Yes there is. classifyTests() uses a method intended to control false 
discovery rate across contrasts. This is not compatible with the simple 
p.adjust() approach to controling FDR across genes. I suggest that you 
simply find what unadjusted p-value corresponds to your desired FDR level 
and enter that to classifyTests().


>I've searched the Bioconductor mailing list but can't find any info on this.
>Jason Skelton
>Pathogen Microarrays
>Wellcome Trust Sanger Institute
>CB10 1SA
>Tel +44(0)1223 834244 Ext 7123
>Fax +44(0)1223 494919
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

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