Thank you for your help Gordon and Dario,

And I agree with you on the last statement, did not realize that yet.

Best regards
Steven WInk


2014-03-08 7:30 GMT+01:00 Gordon K Smyth <smyth@wehi.edu.au>:

> On Fri, 7 Mar 2014, steven wink wrote:
>
>  Did you notice the double brackets? SynergisticEffect =  (AB - control )
>> -*
>> (*(A - control) + (B - control)*)*
>>
>
> Yes, I missed the double brackets.  Your contrast was fine.
>
>
>  To simplify I should write:  AB + C - A - B instead of  (AB - control )
>>
>
> Yes, as Dario has already suggested.  It makes no difference.  Any
> algebraic equation that is equivalent will give the same result in limma.
>
>
>  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)
>>
>
> I don't think that this is really what you mean.  Surely you would want to
> find genes for which the AB effect was in a different direction to the A
> and B effects, even it was not greater in absolute value.  The contrast
> does this.  If what you state is really is what you mean, then this is not
> something you can formally test in limma (or an any other statistics
> program afaik).
>
> Gordon
>
>
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