Thanks Gordon for the helpful reply,I realize why AvsN =
(MutA-ConA)-(MutN-ConN) does not make any sense. I am sorry for that stupid
question, I was out of my mind!

AvsN = ((MUTA-MUTN)+(ConA-ConN))/2. If we do this, I think the log fold
changes would be right but if we do not divide it by two, then the
coefficients or the lfcs would be double even though the t test would give
the same result. Is this right?

Thank you
Jeremy

On Thu, Sep 24, 2009 at 5:12 PM, Gordon K Smyth <smyth@wehi.edu.au> wrote:

> Dear Jeremy,
>
>  Date: Wed, 23 Sep 2009 13:26:57 -0700
>> From: jeremy wilson <jeremy.wilson88@gmail.com>
>> Subject: [BioC] Help on contrast matrix Limma
>> To: bioconductor@stat.math.ethz.ch
>>
>> Hello bioconductor group,
>>
>> I am stuck with understanding how to create contrast matrix for
>> extracting the comparisons I need. Some seem to be easy and some I
>> could never understand. I am analyzing a 2factorial experiment and
>> found the below post useful. I have the exact same questions and would
>> greatly appreciate if any one can give detailed answers.
>>
>> My question from the post below pertains to
>> AvsN=(MUTA+ConA-MUTN-ConN)/2, levels=design)
>>
>> is AvsN also equal to (MutA-ConA)-(MutN-ConN)?
>>
>
> Well, the usual rules of high-school algebra apply.  The formula you've
> written obviously does not have the same value as AvsN.  (You've changed the
> names of the variables, changed the signs, and removed the division by 2.)
>  Why would you think they'd be the same?.
>
>  Also why did we divide the (MUTA+ConA-MUTN-ConN) by 2?
>>
>
> So that AvsN = ((MUTA-MUTN)+(ConA-ConN))/2.  MUTA-MUTN is the effect of
> AvsN on the mutant background.  ConA-ConN is the effect of A on the control
> background.  So AvsN as defined is the effect for A averaged over the mutant
> and control backgrounds.  If you didn't divide by 2 then it would be the sum
> of the effects, which seems somewhat less interpretable. You can choose
> whether you want to divide or not.  It makes no difference to the
> t-statistics or p-values.
>
> Best wishes
> Gordon
>
>  I got this question when I looked at the following code in Limma user
>> guide page 46 with the following code for exact same design
>>
>>  cont.matrix <- makeContrasts(
>>>
>> + WT.SvsU=WT.S-WT.U,
>> + Mu.SvsU=Mu.S-Mu.U,*+ Diff=(Mu.S-Mu.U)-(WT.S-WT.U)*,
>> + levels=design)
>>
>> Hoping to get a response from the bioconductors,
>>
>> Thanks
>>
>> Jeremy
>>
>

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