[BioC] Limma-Contrasts-Question

[Gordon K Smyth]

Dear Biju,

Using the contrast (A1+B1)/2 - (A2+B2)/2 will find genes which response in 
the same direction, and perhaps by about the same fold change, in both A 
and B.

Doing separate tests for A1-A2 and B1-B2, does not require genes to be 
changing in the same direction in A and B.

Best wishes
Gordon

> Date: Thu, 11 Mar 2010 14:49:35 +0100
> From: "Biju Joseph" <bjoseph at hygiene.uni-wuerzburg.de>
> To: <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] Limma-Contrasts-Question
> Message-ID: <000001cac121$b0cbd3b0$12637b10$@uni-wuerzburg.de>
> Content-Type: text/plain;	charset="iso-8859-1"
>
> 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

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