Hi, I am using DEXSeq to identify differential splicing events from RNA-seq data and I did not completely understand how DEXSeq calculates exon usage. It will be really helpful if someone could please explain how DEXSeq calculates exon usage values and how it differs from normalized counts.

Also when I plotted the exon usage values using the plotDEXSeq function, I noticed that the exon usage values on the graph does not correspond with the values from the DEXSeq output files. Could you please help me understand why there is a difference.

Thank you!