In my analysis, I do not want to compare exon based two conditions. I just want to get the expression value for each exon in each sample. How can I do it using DEXSeq?

dxd <- DEXSeqDataSetFromHTSeq(list.files("raw_counts/", full.names=T),
sampleData = sampleTable,
design = ~ 1, # Here is fine?
flattenedfile = "../scrips/genome.gff")

dxd <- estimateSizeFactors(dxd)
dxd <- estimateDispersions(dxd)

What is the next step?

Hi Peter,

What do you mean with expression value for each exon? If you mean the read counts in your exon (maybe normalized for sequencing depth), you could just do:

counts(dxd, normalized=TRUE)

Alejandro

Thanks. The step design = ~ 1 is fine?

Could we use varianceStabilizingTransformation function here?