[BioC] Limma-Contrasts-Question

[Biju Joseph]

Thanks Gordon for your answer.

In my question, I was referring to the DE expressed genes in the same  
direction.

What I am actually unclear about is the following.

Lets say, I generate topTables for
1. A1-A2
2. B1-B2

Now using these 2 individual tables, I could pull out the genes common  
in either direction using lets say Access.

Is this method valid and safe?
How comparable should this manually generated common response between  
strains A and B in conditions 1 and 2 be comparable to the topTable  
generated using (A1+B1)/2 - (A2+B2)/2. Of course I think that these 2  
methods should generate more or less the same results at least with  
respect to numbers of DE genes.

What FC is better to report for the common response? One from using  
the (A1+B1)/2 - (A2+B2)/2 contrast or the FC from the individual  
topTables.

Best
Biju


Quoting Gordon K Smyth <smyth at wehi.EDU.AU>:

> 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
>>
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