Hello all,

I am working with data with a very large number of differentially expressed
genes (liver cancer samples), and wish to demonstrate for my advisor and
committee the effect of choosing different pre-processing methods.  To do
this, I have normalized the data in several different ways and genereated
DEG lists with limma and decideTests.   Now I would like to examine the
difference in which probesets are called by the various methods.

I've read everything I can find about the venn tools in limma and
vennSelect, but they only seem to compare the output of different contrasts
within a single dataset.  Can someone suggest how to compare the output of
the same contrast in a dataset processed 2 ways?  I could output to
Microsoft Access, but surely there is a better way!!

Thanks so much,
Mikki Behnke
Integrative Life Sciences
Virginia Commonwealth University

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