[BioC] Limma-Contrasts-Question

[Biju Joseph]

Dear all

Sorry if this is a trivial question,
My experiment design is the following
2 strains (A & B) subjected to 4 conditions each (1,2,3,4) compared using a
common reference design.
We are interested in various contrasts between the 8 samples.
Using limma - I was able to generate topTables for the required contrasts
eg:
A1-B1, A2-B2, A3-B3, A4-B4
A1-A2, A2-A3, B1-B2, B2-B3 and so on

A comparison for example the topTable A1-A2 and B1-B2, would represent the
common response in A and B from condition 1 and condition 2.

Using this manual comparison of the 2 topTables, I saw that around 400 genes
are commonly differentially regulated in strain A and strain B in the
conditions 1 and 2.

Now when I include the following contrast in my model in limma 

(A1+B1)/2 - (A2+B2)/2 which in my understanding also generates the common
response between condition 1 and 2 in the 2 strains A and B.

The topTable generated using this contrast shows only 10 genes to be
commonly differentially regulated between condition 1 and 2.

Would be great if someone could explain this discrepancy to me and about
which method is safer to compare(comparison of the 2 individual toptables or
the toptable generated using make.contrasts).

Best
Biju
Institut für Hygiene und Mikrobiologie
Universität Würzburg
Josef-Schneider-Str. 2, Gebäude E1
97080 Würzburg
Email: bjoseph at hygiene.uni-wuerzburg.de
Tel.:    0931 201 46708
Fax:    0931 201 46445