[BioC] venn diagram

Gordon Smyth smyth at wehi.edu.au
Thu Apr 29 00:45:16 CEST 2004

At 06:41 PM 28/04/2004, Anthony Bosco wrote:
>I actually want to compare lists of gene names (not expression data) using 
>venn diagram tools.
>For example if I have a cell line and stimulate with several different 
>treatments I want to know which genes are differentially expressed in all 
>treatments or only some of the treatments.

Mmm, judging which genes are differentially expressed without considering 
expression data would be a good trick! :)

There is an example of using venn diagrams for the purpose you describe in 
the User's Guide of the most recent versions of limma. If you're using R 
1.8.1, get limma from http://bioinf.wehi.edu.au/limma, if you're using R 
1.9.0, get it from the BioC development area.


>I would also like to look at this graphically to get an overview of which 
>treatments are more similar.
>I realise that heatmap functions etc would show similarities/differences 
>b/w treatments but in this particular case I want to use venn diagrams.
>Anthony Bosco - PhD Student
>Institute for Child Health Research
>(Company Limited by Guarantee ACN 009 278 755)
>Subiaco, Western Australia, 6008
>Ph 61 8 9489  , Fax 61 8 9489 7700
>email anthonyb at ichr.uwa.edu.au
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

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