[BioC] What does this mean in Limma?

[Davide Cittaro]

On Feb 3, 2013, at 12:57 AM, Gordon K Smyth <smyth at wehi.EDU.AU> wrote:

> Dear Davide,
> 
> The short answer is that you shouldn't be interpreting the fit3 results 
> because they are probably not want you want.
> 
> You have fitted a linear model in which there is no intercept, but instead 
> three coefficients representing the means of the three groups.  If you 
> simply display the results of topTable(fit3), then limma will test whether 
> any of the coefficients are equal to zero.  This will select genes that 
> have mean log-intensities in any group greater than zero.  So you are 
> simply getting a list of highly expressed genes, not genes that are 
> differently expressed between your groups.
> 

Thanks, that's much clearer now

d

> Best wishes
> Gordon
> 
> 
>> Date: Fri, 1 Feb 2013 22:12:35 +0100
>> From: Davide Cittaro <cittaro.davide at hsr.it>
>> To: "bioconductor at r-project.org" <bioconductor at r-project.org>
>> Subject: [BioC] What does this mean in Limma?
>> 
>> Hi all,
> 
>> I'm performing an analyis in limma with 3 groups. Normally I would set 
>> up a simple analysis with 3 contrasts:
>> 
>> groups <- factor(c(A,A,A,B,B,B,C,C,C))
>> design <- model.matrix(~0+group)
>> contrasts <- makeContrasts(B-A, C-A, C-B, levels=design)
>> fit <- lmFit(y, design)
>> fit2<-eBayes(contrasts.fit(fit, contrasts))
>> 
>> Because of an error, I've didn't set the matrix and performed
>> 
>> fit3<-eBayes(fit)
>> 
>> In which way I should interpret the results in fit3 (which, by the way, 
>> are really interesting)?
>> 
>> Thanks
>> 
>> d
>> 
> 
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