[BioC] Gene names in limma Venn Diagrams

[James Wettenhall]

Christine,

On Tue, 23 Sep 2003 c.chaffer at pgrad.unimelb.edu.au wrote:
> Hi James,
> 
> How's it going?  I have a question for you!!
> 
> I've been playing with my data in Limma and am wondering if there is a way 
> to get a list of the genes that are represented in the intersection of the 
> venn diagram??

Use classifyTests to get a classification object "clas" which 
you can use in vennCounts.

Then you can use :
clasWithGenes <- cbind(genelist,clas$classification)
to combine the genelist information with the classification. 
Make sure that nrow(genelist)==nrow(clas$classification).  
If not, you might need to run unwrapdups on genelist.

Then to see only the rows of clasWithGenes with genes 
upregulated in both comparisons, use :
clasWithGenes[clasWithGenes[,"Control-Ref"]==1&clasWithGenes[,"KO-Control"]==1,]

The number of rows of this result should be the same as the 
corresponding count in 
vennCounts(clas,include="up")

Regards,
James