[BioC] Contrast matrix in limma

[Ingunn Berget]

Thank you!
(and yes I mean sum to zero)

ingunn

----- Original Message ----- 
From: "Gordon K Smyth" <smyth at wehi.EDU.AU>
To: "Ingunn Berget" <ingunn.berget at umb.no>
Cc: <bioconductor at stat.math.ethz.ch>
Sent: Tuesday, February 15, 2005 1:31 PM
Subject: [BioC] Contrast matrix in limma


>> Date: Mon, 14 Feb 2005 12:41:22 +0100
>> From: "Ingunn Berget" <ingunn.berget at umb.no>
>> Subject: [BioC] Contrast matrix in limma
>> To: <bioconductor at stat.math.ethz.ch>
>>
>> Dear BioC-list
>>
>> I have data from a microarray experiment comparing 12 different growth 
>> conditions for bacteria.
>>
>> This are the conditions
>> BC7ppm BC9ppm CH3COOH EtBr EtOH Glycerol gr15 gr46 HCl NaCl NaOH PK
>>
>> PK is the normal condition and it is of interest to find genes that are 
>> differentially expressed
>> in PK and the other conditions. The experiment is a reference design with 
>> common reference for all
>> arrays, and with three biological replicates from each condition. The 
>> reference is always labelled
>> Cy3. The two conditions BC7ppm and BC9ppm represent the same medium for 
>> the bacteria, but with
>> different concentrations of something.
>>
>> If I have understood the limma usermanual correctly, the following lines 
>> will make all contrasts
>> for comparing gene epression in one condition with PK such that the 
>> contrast names BC7.PK compares
>> geneexpression in BC7ppm condition with PK and BC9.PK gene expression in 
>> BC9ppm with PPK.
>> D <- modelMatrix(MA$target,ref = "Ref") #MA is the MAlist with the 
>> normalised data
>>
>> contrast.matrix <- 
>> makeContrasts(gr15.PK=gr15-PK,gr46.PK=gr46-PK,NaCl.PK=NaCl-PK,EtBr.PK=EtBr-PK,
>> EtOH.PK=EtOH-PK,NaOH.PK=NaOH-PK,CH2COOH.PK=CH3COOH-PK,HCl.PK=HCl-PK,BC7.PK=BC7ppm-PK,
>> BC9.PK=BC9ppm-PK, Gly.PK=Glycerol-PK,levels=D)
>>
>> Since there is very little difference between BC7ppm and BC9ppm, I want 
>> to "merge" these to
>> experiments and make one contrast for both. So my questions are
>>
>> 1) can I do this?
>>
>> 2) In general the sum of the coefficients in a contrast should be one,
>
> I think you mean, sum to zero.
>
>> does this mean that I
>> should use something like
>>
>> BC.PK= 0.5*BC7ppm+0.5*BC9ppm-PK
>>
>> as an argument in the makeContrasts command?
>
> Yes, it sounds as if this is what you need.  Your contrast BC.PK compares 
> PK to the average of
> BC7ppm and BC9ppm, which sounds like what you're after.
>
> Gordon
>
>> Best regards
>>
>> Ingunn
>
>