rSeqDiff: Detecting Differential Isoform Expression from RNA-Seq Data Using Hierarchical Likelihood Ratio Test
Figure 3
Comparisons of rSeqDiff, MATS, Cuffdiff 2 and RT-PCR assays.
(A) Scatter plot of the Δψ values estimated by rSeqDiff (using junction reads only) and MATS. (B) Scatter plot of the Δψ values estimated by rSeqDiff (using junction reads only) and RT-PCR. (C) Scatter plot of the Δψ values estimated by rSeqDiff (using all reads) and RT-PCR. (D) Scatter plot of the log2 fold changes of isoform abundances between ESRP1 and EV estimated by rSeqDiff and Cuffdiff 2. Transcripts classified as model 0, model 1 and model 2 are shown in green, blue and red, respectively. The solid line is the regression line. The dashed line is the y = x line, which represents perfect agreement of the two methods. Δψ: difference of exon inclusion level between ESRP1 and EV; PCC: Pearson Correlation Coefficient; SCC: Spearman Correlation Coefficient.