I have followed the Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification vignette to analyze my data and had no problems. Specifically, I used DEXseq followed by stageR. However, I was hoping to get fold changes for individual transcripts that show evidence for DTU. The only output I get are the pvalues for each transcript. Is it possible to do this? I did not include code since I did not have problems with the code, but I'm happy to post if it would be helpful. Thanks!

This object will have per transcript log fold changes:

dxr <- DEXSeqResults(dxd, independentFiltering=FALSE)