Question: Normalized transcript/exon counts for network analysis
0
gravatar for maya.kappil
9 months ago by
maya.kappil10
maya.kappil10 wrote:

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

dexseq sva wgcna drimseq • 264 views
ADD COMMENTlink modified 9 months ago by Gosia Nowicka40 • written 9 months ago by maya.kappil10
Answer: Normalized transcript/exon counts for network analysis
1
gravatar for Gosia Nowicka
9 months ago by
Basel
Gosia Nowicka40 wrote:

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.

ADD COMMENTlink written 9 months ago by Gosia Nowicka40

Ah, ok - that makes sense! Thanks!!

ADD REPLYlink written 9 months ago by maya.kappil10
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