[BioC] comparing two or more limma::topTables - in search of a graphical tool

[James W. MacDonald]

Hi Massimo,

Massimo Pinto wrote:
> Greetings all,
> 
> in an experiment which I have analyzed using a factorial design, I
> have reached a point where I have produced a number of fits to my data
> with several contrasts and I am interested in making some comparisons
> between the two or more lists of differentially expressed genes. One
> tool, as I understand, is to make a VennDiagram based on
> limma::decideTests(). However, this has the limitation that the IDs of
> the differentially expressed genes are lost in the diagrams (but I can
> still manually look in the list produced by decideTests), and if one
> gene is upregulated in one contrast but down-regulated in another
> contrast, this gene won't appear in the intersection of the two
> circles of the Venn Diagram. This information, however, may be
> interesting and noteworthy.

This last statement is incorrect. The default behavior of vennCounts() 
is to include both up and down regulated genes in the intersection. This 
includes genes up-regulated in one contrast and down-regulated in the other.


> 
> What graphical tools do exist to assist an investigator in this part
> of data analysis?

I don't know what other graphical tools would be useful. Certainly 
listing a bunch of gene IDs in a Venn diagram would not be particularly 
useful.

If you want annotated tables of the genes in each cell of the Venn 
diagram, the vennSelect() function in affycoretools may be of use (if 
you are using Affy chips). If you are using a different platform, the 
vennSelectBM() function may be useful.

Best,

Jim


> 
> Thank you in advance,
> Massimo
> 
> Massimo Pinto
> Post Doctoral Research Fellow
> Enrico Fermi Centre and Italian Public Health Research Institute (ISS), Rome
> http://claimid.com/massimopinto
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
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1241 E. Catherine St.
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