Fig. 4.

An example of rMATS unpaired analysis of prostate cancer cell lines. (A) The RNA-Seq read counts and estimated exon inclusion levels of ARHGAP17 exon 15 in a pair of epithelial (PC3E) and mesenchymal (GS689) cell lines, each with three biological replicates. (B) The log likelihood of observing the data given all possible combinations of ${\psi }_{i1},{\psi }_{i2}$. In this likelihood-ratio test, the null hypothesis is $\left|{\psi }_{i1}-{\psi }_{i2}\right|\le 5\%$ and the alternative hypothesis is $\left|{\psi }_{i1}-{\psi }_{i2}\right|>5\%$. The combination of ${\psi }_{i1},{\psi }_{i2}$ that maximizes the likelihood of observing the data under the constraint of the null hypothesis or without such a constraint is indicated.