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

[Gordon K Smyth]

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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