Hi!

I would like to generate a cosplicing network similar to how it's described here (https://github.com/iancuo/cosplicingNetworks). My understanding is that I would need normalized exon/transcript counts prior to generating the network. For DEXSeq, I was planning to input the normalized exon counts from the DEXSEqDataSet generated as follows:

dxd <- DEXSeqDataSet(countData=count.data, sampleData=sample.data, design=~sample + exon + group:exon, featureID=counts(d)$featureid, groupID=counts(d)$geneid)

system.time({ dxd <- estimateSizeFactors(dxd) dxd <- estimateDispersions(dxd, quiet=TRUE) dxd <- nbinomLRT(dxd, reduced=~sample + exon) })

dxd_norm<-counts(dxd,normalized=T)

I was wondering whether a similar option is available to output normalized transcript levels from DRIMSeq?

Thanks!

Maya

Hello Maya,

no, there is no way to get normalized data from the DRIMSeq workflow. This is because DRIMSeq does not need to use normalized data when comparing proportions.

What you could do is to input your transcript counts into DEXSeq in the same way you did with exon counts.