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Table 3 Median percent error (MPE) and 15% error fraction (EF.15) for gene expression levels inferred from 30 M reads of length 25 simulated assuming geometric isoform expression.

From: Estimation of alternative splicing isoform frequencies from RNA-Seq data

Expression range (0, 10-6] (10-6, 10-5] (10-5, 10-4] (10-4, 10-3] (10-3, 10-2] All
# genes 120 5,610 11,907 1,632 102 19,372
  Uniq 37.4 43.6 42.7 43.0 48.2 43.0
  Rescue 32.8 28.7 26.0 25.1 28.8 26.7
MPE GeneEM 30.6 28.2 25.7 25.1 28.0 26.3
  Cufflinks 33.0 21.1 19.0 20.2 40.2 19.7
  RSEM 23.6 11.0 7.2 7.9 11.4 8.1
  IsoEM 18.2 8.4 3.2 2.0 1.9 3.9
  Uniq 77.5 82.4 81.7 79.7 82.4 81.7
  Rescue 74.2 74.0 71.6 72.8 76.5 72.4
EF.15 GeneEM 72.5 73.8 71.5 73.0 74.5 72.3
  Cufflinks 73.3 64.7 62.3 66.2 82.3 63.5
  RSEM 64.2 37.3 17.4 16.3 41.2 23.5
  IsoEM 57.5 28.1 6.7 6.1 4.9 13.2