[miso-users] Question on Filtering Differentially Expressed Events

[Gao, James (NIH/NCI) [E]]

Dear Yarden,

Could you please elaborate on the example you gave in the manual on how to
filter differentially expressed events?

Below are the command and the explanation of the options:
======

python filter_events.py --filter control.miso_bf --num-inc 1 --num-exc 1
--num-sum-inc-exc 10 --delta-psi 0.20 --bayes-factor 10 --output-dir
filtered/


For example, to filter the file control.miso_bf to contain only events
with: (a) at least 1 inclusion read, (b) 1 exclusion read, such that (c)
the sum of inclusion and exclusion reads is at least 10, and (d) the Δ Ψ
is at least 0.20 and (e) the Bayes factor is at least 10, and (a)-(e) are
true in one of the samples.


======

Here are the questions I have:

1) Does using "--num-inc 1 --num-exc 1 --num-sum-inc-exc 10" meaningful
biologically? 
2) In "(a)-(e) are true in one of the samples", should be (a)-(c)? I think
(d) and (e) are calculated based on both samples.
3) Is it possible for the Δ Ψ value to be negative? If so, how significant
to have a value of 0.20?
4) In the manual, it sated "For example, a Bayes factor of 2 would mean
that the isoform/exon is two times more likely to be differentially
expressed than not", then is the "--bayes-factor 10" to stringent?

Thank you very much for your help.

James