[BioC] LIMMA makeContrasts question

[kfbargad at ehu.es]

Dear TS,

I am a biologist and found "Design and Analysis of Experiments" by DC 
Montgomery very useful, although it is not a manual on how to make 
contrasts

HTH

David


> Dear TS,
> 
> You are wanting to select genes which satisfy several conditions. 
> There is no way to do this with a single contrast. You need to 
> compute all three contrasts and then select genes:
> 
> cm = makeContrasts(ON=ON-WT, KO1=KO1-WT, KO2=KO2-WT, levels=design)
> fit <- lmFit(data, design)
> fit2 <- contrasts.fit(fit, cm)
> fit2 <- eBayes(fit2)
> results <- decideTests(fit2)
> selectedgenes <- results[,"ON"]*results[,"KO1"]== -1 & 
> results[,"ON"]*results[,"KO2"]== -1
> sum(selectedgenes)
> write.fit(fit2[selectedgenes,], file="myresults.txt")
> 
> Unfortunately I don't know of any good introductions to linear 
models 
> which are suitable for a biology audience.
> 
> Best wishes
> Gordon
> 
> >Date: Thu, 30 Nov 2006 21:23:15 -0500
> >From: "T S" <tsm8015 at gmail.com>
> >Subject: [BioC] LIMMA makeContrasts question
> >To: bioconductor at stat.math.ethz.ch
> >Message-ID:
> >         
<4a912b5b0611301823n5be74787o2e249ec9657041b6 at mail.gmail.com>
> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> >Hi,
> >
> >I am a complete beginner to Linear Models and using the LIMMA 
package.
> >First I have a general question as to what are good intro texts
> >explaining Linear Models in general.
> >
> >I also have the following specific question. I have 4 samples: wild
> >type (WT), a sample were I turn on a pathway (ON) and two where I
> >knock down the same pathway in two different ways (KO1, KO2). I want
> >to find genes that are significantly changed with the following
> >property:
> >
> >    sign(log(ON/WT)) == -sign(log(KO1/WT)) and -sign(log(KO2/WT))
> >
> >would the following design and contrast matrix be correct
> >
> >type = is a factor with levels WT, ON, KO1, KO2
> >design = model.matrix(~0 + type)
> >cm = makeContrasts(eff = (ON - WT) - (KO1 - WT) - (KO2 - WT), 
levels=design)
> >
> >Any help or guidence would be greatly appreciated. Also pointers to
> >suitable documentation explain such matters would be great.
> >
> >Thanks in advance
> 
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