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Table 2 Recall and precision at P adj =0.05 measured under all simulation studies

From: Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems

  Cufflinks DEXSeq MATS SpComp rDiff-param DiffSplice SeqGSEA
  Rec. Prec. Rec. Prec. Rec. Prec. Rec. Prec. Rec. Prec. Rec. Prec. Rec. Prec.
High 100x Diff 0.57 0.91 0.53 0.65 0.28 0.98 0.14 0.95 0.06 0.99 0.24 0.79 - -
Medium 100x Diff 0.40 0.91 0.31 0.71 0.22 0.98 0.08 0.90 0.02 0.95 0.24 0.76 - -
Low 100x Diff 0.03 0.77 0.06 0.59 0.1 0.99 0.02 0.82 0.002 0.833 0.20 0.66 - -
High 100x Same 0.58 0.90 0.49 0.71 0.27 0.98 0.13 0.94 0.05 1.0 0.26 0.84 - -
Medium 100x Same 0.42 0.91 0.25 0.80 0.21 0.99 0.07 0.92 0.01 1.0 0.25 0.81 - -
Low 100x Same 0.15 0.91 0.04 0.96 0.08 0.99 0.02 0.84 0.001 1.0 0.21 0.68 - -
100x High Diff 0.57 0.91 0.53 0.65 0.28 0.98 0.14 0.95 0.06 0.99 0.24 0.79 - -
60x High Diff 0.49 0.91 0.29 0.72 0.22 0.99 0.09 0.93 0.02 1.0 0.25 0.81 - -
25x High Diff 0.39 0.92 0.22 0.75 0.15 0.98 0.06 0.93 0.008 0.94 0.17 0.79 - -
A3A5SS 0.73 0.95 0.71 0.71 0.85 1 0.04 0.875 0.01 1 0.07 0.85 - -
IR 0.69 0.95 0.43 0.8 0.76 0.99 0.09 0.8 0.09 1 0.36 0.82 - -
SE 0.67 1 0.71 0.91 0.85 1 0.38 1 0.04 1 0 0 - -
Complete annot. 0.57 0.91 0.53 0.65 0.28 0.98 0.14 0.95 0.06 0.99 0.24 0.79 - -
Incomplete annot. 0.67 0.92 0.14 0.41 0.08 0.97 0.12 0.93 0.008 0.94 0.24 0.79 - -
8samples 0.65 0.81 0.66 0.55 0.3 0.93 0.50 0.82 0.06 0.99 0.17 0.72 0.95 0.58
  1. A3A5SS stands for the joint class of alternative 3’ splice site event and alternative 5’ splice site event. IR stands for intron retention event and SE stands for skipping exon event. Recalls were shown as the numbers in the left column, precisions in the right column. Larger values of both metrics are better. Under a sample size of 3, SeqGSEA found no genes at P adj =0.05 and therefore no values were reported.
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