[BioC] Lumi/Limma - Get nuIDs and expression intensities in result

[Atul Kakrana]

Hi All,

I am analyzing the Illumina data and need to add expression intensities 
in the final results. At this moment output from Limma does not include 
normalized expression intensities for all samples. I was suggested to 
use 'Limma2anaaffy' from 'affycoretools' but unfortunately it does not 
work on Illumina data.Could somebody please suggest me how can I add 
expression intensities to final output?

One way I see it is to get the IDs from final result and than extract 
expression intensities for those IDs from the normalized data. Finally, 
I can manually add expression intensities to the final result using 
Excel. But problem is that in illumina results from 'decideTests' Nu Ids 
are missing, which are present in expression set. So is there any way to 
add NuIds to final results?

Simplified code:

mydata<- lumiR.batch(filename)
lumi.N.Q <- lumiExpresso(mydata, 
normalize.param=list(method='rankinvariant'))
sampletype <- c('1','1','2','2','3','3')
group <-factor(sampletype)
design<- model.matrix(~0+group)
fit <- lmFit(esetLumi.Reduced, design)
fit2 <- eBayes(fit2)
results.default <- decideTests(fit2)
write.fit(fit2,results.default,file='RESULTS2.tsv', sep = '\t')

Please suggest me how can I add expression intensities to the final 
result output file? Or at least how can I have nuIDs in my final results?

Thanks

AK