I am a bit confused.
I compared differentially expressed spliced transcripts between a sample 1 and a sample 2 using MISO algorithm.
The final (filtered) result table notably mentions the following info (this is an example for a transcript with 3 isoforms):
. delta PSI: -0.67,0.19,-0.87
. isoforms: isoform1,isoform2,isoform3 (isoform 1 is the inclusive form (with all exons); isoforms 2 and 3 are spliced)
According to MISO paper:
. PSI is the fraction of the inclusive transcript in a sample (i.e. not spliced if I understand well)
. delta PSI = PSI(sample1) - PSI(sample2)
Thus, for example:
. delta PSI(isoform1) = -0.67 means there are more inclusive transcript in sample 2 than sample 1,
. delta PSI(isoform2) = 0.19 means there are more inclusive transcript in sample 1 than sample 2, but how is it related to isoform2 which is known to be spliced? Does MISO report only the spliced isoforms in its output?