Hi Alex,
This is not an issue but rather a question about one of the parameters of SpliceWiz.
To get significant differential events, I saw in the quick start tutorial of SpliceWiz, we can obtain a list of differential events with delta PSI > 5%, res_limma.filtered <- subset(res_limma, abs(deltaPSI) > 0.05). My question is that if I use deltaPSI > 0.2 would that mean the differential events between condition B versus A are more confident than deltaPSI >0.05?
I would highly appreciate your time and comments.
Best regards
Reza
Code should be placed in three backticks as shown below
"Confidence" is often synonymous with statistical significance which is measured as p-values. In context of multiple testing, the adjusted p value is favored.
Sometimes, adding a filter of |delta PSI| is helpful to avoid including events with PSIs at the limit margins. E.g. if in control, PSI = {0.0001, 0.00009, 0.00011} and in treatment PSI = {0.0010, 0.0011, 0.0012}, it will be called as highly statistically significant although at the protein translation level this may be functionally meaningless. There is no set rule as to what |delta PSI| filter to use, but in my experience, > 0.2 is too high.
However, for cherry-picking "top" results then |delta PSI| > 0.2 might be useful.