Hi,

I want to construct sampleTable and design and ultimately the exon fold change in between all three conditions namely F, LR and LR. Here I used the code in DEXseq package of R. The input data is counts.txt file from FeatureCounts Here I used the code

sampleTable = data.frame(
  row.names = c("F1","F2","LR1","LR2","LV1","LV2"),
  condition = factor(rep(c("F","LR","LV"),each=2)),
  libType = c("paired-end","paired-end","paired-end", "paired-end","paired-end", "paired-end"))

sampleTable
dxd <- DEXSeqDataSet(cc,design=~sample + exon + condition:exon, featureID=as.factor(exon_ids),
                     groupID=as.factor(clusters),sampleData=sampleTable)

but I only get 'exon fold change' in between F,LR and F,LV but I could not get the exon fold change between LV,LR. kindly suggest the solution for the same.

Thank you in advance,

Aniket.