Many of the tools I've used provide insight into differences in splicing events or DTE/DTU between conditions, but what if I want to make comparisons (with some measure of confidence) between isoform abundances within conditions. Could I just use the estimated abundance of each transcript from Salmon quantification corresponding to a gene of interest? If so, what statistical test would be appropriate for the comparison? The null hypothesis, here, is that all expressed (vs. annotated?) isoforms contribute equally to the total gene abundance. Would an Anova + (paired?) Student's t-test with some kind of p-value correction be valid here?

Thanks, Nico

My preferred approach would be to estimate the proportion vector p within a condition with either posterior SD or SE on the components of p.

Given that the null hypothesis is trivially false for many (all?) genes, I think the p with bands on each component is sufficient for describing one gene.

I think there should be a way to propagate from e.g. DRIMSeq estimated precision to the uncertainty on p. I'll try to bring this thread to the package authors' attention.