Hi If you are comparing categorical data such as this, maybe try Multiple Correspondence Analysis (available in the ade4 package). Aedin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch]On Behalf Of Arne.Muller@aventis.com Sent: 28 April 2004 10:17 To: anthonyb@ichr.uwa.edu.au; bioconductor@stat.math.ethz.ch Subject: RE: [BioC] venn diagram Hi, The problem with Venn diagrams is that for > 3 sets the visualization it gets messy. Maybe you can just go for a tabular representation instead of graphics. With a dendogram you could viz. your genelist similarity using vector similarity. Take the union of all m sets. This is a super set with n elements. Create a m*n matrix (m columns) where the row names represent gene names. The value for each cell is either 0 or 1 depending whether the gene x is present in set y. You can then create a distance matrix from this by calculating all pariwise combinations of the length normalized cosine between the vectors: > a <- c(1,1,0,0,1,0) > b <- c(0,1,1,0,1,1) > x <- a%*%b / (length(a) * length(b)) > x [,1] [1,] 0.05555556 x is a measure for the similarity between vectors a and b. This is used is a standard procedure in text/document comparison. Since one want s to create a distance matrix one still needs to somehow "invert" this matrix so that high similqrity gets small values! Once you've your matrix M of cosines (this is a symmetric matrix m). You convert this via as.dist(M), and pass it to the hclust routine. I'd be interested in the outcome (does it make sense?) - if you're interested. You should only try it if you've got *many* sets to test, so that a real Venn approach gets too complex. good luck and let me know how it goes, +regards, Arne -- Arne Muller, Ph.D. Toxicogenomics, Aventis Pharma arne dot muller domain=aventis com > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch]On Behalf Of Anthony > Bosco > Sent: 28 April 2004 10:41 > To: bioconductor@stat.math.ethz.ch > Subject: [BioC] venn diagram > > > Hi. > > 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. > > 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. > > > Regards > > > Anthony > -- > ______________________________________________ > > 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@ichr.uwa.edu.au > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor