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?
Can I ask how you filtered your output when your sample has more than two isoforms? I'm aware that the documentation allows you to filter using the filter_events script, but thats only for two isoform events. You can filter on bayes-factor on >2 isoform events but this still outputs an note/error for me: "filter_events: filtering MISO pairwise comparison output.
Note: This utility is only works on MISO output for two-isoform event annotations.
Error: filter_events.py is only defined for MISO output on two-isoform alternative events. Found a non-two isoform event: ENSMUSG00000032469"