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

[Massimo Pinto]

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.

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

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