Entering edit mode
Biju Joseph
▴
30
@biju-joseph-3955
Last seen 10.5 years ago
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 f?r Hygiene und Mikrobiologie
Universit?t W?rzburg
Josef-Schneider-Str. 2, Geb?ude E1
97080 W?rzburg
Email: bjoseph at hygiene.uni-wuerzburg.de
Tel.: 0931 201 46708
Fax: 0931 201 46445