Entering edit mode
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
______________________________________________________________________
The information in this email is confidential and
intend...{{dropped:4}}
