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

[Atul Kakrana]

Hello Gordon,

Many thanks. There could be million ways but you told me the one that is
probably the best.

AK

On 05/01/2013 10:39 PM, Gordon K Smyth wrote:
> Dear Atul,
>
> There are a million ways to add columns of annotation.
>
> For example, you could add the Intensities to the gene annotation
> data.frame:
>
>   fit2$genes <- data.frame(fit2$genes,Intensities)
>
> so that the intensities will appear in any output table from limma.
>
> Best wishes
> Gordon
>
> ----------- original email ---------------
> [BioC] Limma/Affy - Include expression Intensity in Final
> 'decideTests' results Atul Kakrana atulkakrana at outlook.com
> Mon Apr 29 05:55:39 CEST 2013
>
> 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?
>
> AK
>
>
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