Question about dPSI threshold value

[Matthew Wright]

Hi,

I apologize if this has been asked before, I am just trying to understand the logic behind the filtering threshold of the abs(E(dPSI)) value. Attached is an LSV which is filtered out using the default abs(E(dPSI)) threshold of 0.2, but appears when I lower the threshold to 0.1 (also appears when I lower the threshold to 0.19 on the voila view page). I would think that since one of the junctions has E(dPSI) of 0.215, this LSV should pass at either threshold, so I am wondering what else is going on for this to be filtered out? Any guidance would be helpful.

I am using MAJIQ v 2.2.0-e25c4ac. majiq build was run with --simplify and --min-intron-cov 1, followed by majiq deltapsi on my two groups. The values in the TSV were obtained with voila tsv --probability-threshold 0.95 --threshold 0.1. I'm happy to provide more details if anything here is not clear.

Thank you,

Matt

Voila TSV

Voila View

[Paul Jewell]

Hi Matt,

Voila view provides both a raw dpsi value threshold and also statistical confidence threshold when running in dpsi mode. In order to show up on the index page the LSV must pass BOTH thresholds. Have you tried raising / lowering the confidence as well?