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

[Maciej Jończyk]

Hi Atul,
>
> 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?

You could try make new object with binded columns with fold-changes.

If you used BH p-value correction and "separate" method you could 
write:

result_table=cbind(fit2$coefficients,fit2$p.value,p.adjust(fit2$p.value,"BH"),separate)

So you'll get table with: gene id, fold-change (coefficients), p-value, 
adjusted p-value, significance code.


Where "separate" is a result of:
separate=decideTests(fit2,method="separate",adjust.method="BH",p.value=0.05)

HTH,
Maciej

>
> AK

-- 
Dr Maciej Jonczyk,
Department of Plant Molecular Ecophysiology
Faculty of Biology, University of Warsaw
02-096 Warsaw, Miecznikowa 1
Poland


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