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

Simone from Mark Robinson's group has an answer for you: