[BioC] Lumi/Limma - Get nuIDs and expression intensities in result
Atul Kakrana
atulkakrana at outlook.com
Tue Apr 30 18:56:04 CEST 2013
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
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