[BioC] Limma/Affy - Include expression Intensity in Final 'decideTests' results

[James W. MacDonald]

Hi Atul,


On 4/28/2013 11:55 PM, Atul Kakrana wrote:
> Hi All,
>
> I am using 'affy' and 'limma' to analyze affymetrix data.
>
> Simplified code:
>
> mydata <- ReadAffy()
> esetRMA <- rma(mydata)
> sampletype <- c('1','1','1','2','2','2','3','3','3','4','4','4')
> group <-factor(sampletype)
> design<- model.matrix(~0+group)
> fit <- lmFit(esetRMA, design)
> contrast.matrix<-makeContrasts(B-A,C-A,D-A, levels=design)
> fit2<- contrasts.fit(fit,contrast.matrix)
> fit2 <- eBayes(fit2)
> results.default <- decideTests(fit2)
>
> I get the results without any problem. But what I need is expression 
> intensity of probes across all samples to be included in the results. 
> I tried:
> Intensity <- (2^(exprs(esetRMA)))
>
> But cannot fit data to the results
> fData(results.default) <- Intensity
>
> Could somebody please tell me how can include expression intensities 
> in the 'decideTests' output?

The output from decideTests() is just a matrix of 0 and 1, so you 
wouldn't want to append anything to that to begin with.

You might take a look at limma2annaffy() in affycoretools, which does 
essentially what I think you want.

Best,

Jim


>
> AK
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099