Did you notice the double brackets? SynergisticEffect =  (AB - control ) -*
(*(A - control) + (B - control)*)*

If I change the "+" to a "-" I get
AB + C - A +  B
The model becomes
 aver.gene.expr=â1*X_AB +  â2*X_C -  â3*X_A +  â4*X_B + error, with  â the
average gene expression of each group and X_xx the respective rows of the
contrast matrix.
I don't see any suitable way to test any hypothesis here I am interested in.

I would like to find significant genes where  abs(log2_FC(AB))  >> abs(
log2_FC(A) + log2_FC(B) ), where FC is fold change as compared to control
(C)


To simplify I should write:  AB + C - A - B instead of  (AB - control ) -
* (*(A - control) + (B - control)*)*
if H0: â1 + â2 = â3 + â4 is rejected I have my genes (I believe)




2014-03-07 0:20 GMT+01:00 Gordon K Smyth <smyth@wehi.edu.au>:

> Dear Steven,
>
>  Date: Wed, 5 Mar 2014 13:42:34 +0100
>> From: steven wink <hardervidertsie@gmail.com>
>> To: <bioconductor@stat.math.ethz.ch>
>> Subject: [BioC] limma contrast matrix interaction effect
>>
>> Dear list,
>>
>> I was hoping for some input since I have difficulty figuring out if I
>> obtain a valid DEG for my biological question.
>>
>> By following the limmaUsersGuide manual I came up with a modification that
>> might be suitable for my analysis.
>>
>> I have 4 treatments: control, A, B and AB
>> so AB is a combined treatment of  A and  B
>> After defining my design matrix I set up contrasts:
>>
>> SynergisticEffect =  (AB - control ) - ((A - control) + (B - control))
>>
>> Would this contrast give me a DEG where I want to test if the combined
>> treatment has more effect than the sum of individual treatments?
>>
>
> It would be correct if you changed the "+" to "-".
>
>  Would I first have to test for main effects before stating significant
>> interaction effects? Does this in effect mean I should remove genes from
>> DEG obtained from interaction test that are also in DEG of main effects (ie
>> A-control or B-control and also AB-control)?
>>
>
> No, there is no need whatsoever to do this.
>
> Best wishes
> Gordon
>
>  Any help on making this more clear for me is greatly appreciated!
>>
>> Best regards,
>> Steven
>>
>
> ______________________________________________________________________
> The information in this email is confidential and inte...{{dropped:10}}

