> 0.5 and PSI > 0.01 in more than 50% of the samples) and sufficiently well-estimated PSI (standard deviation across MISO iterations of PSI estimate < 0.1, and a coefficient of variation on the estimate < 0.5 in more than 50% of samples). After filtering, a total of 43,817 isoforms of 12,329 genes remained for analysis. The covariate model used for gene analyses was used for isoform-level analyses. As a technical assessment of self-consistency, For 85% of the analyzed isoforms, the correlation across samples between the number of unique reads per isoform, arguably, the most direct measure of relative isoform abundance from RNA-seq, and the isoform-level CPM was above 0.2. Analyses for discovery of differential isoform expression and isoform-eQTL association used a strategy analogous to that at the gene level. Of note, we estimated isoform-level voom sampling weights from the isoform log(CPM) data and then used these weights in all linear regression analyses..
