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Table 3 Consistency between transcript abundance estimated by different methods and gold standards in Dataset 2.

From: PDEGEM: Modeling non-uniform read distribution in RNA-Seq data

  RPKM MART PDEGEM
R 2 − 1 0.30 0.54
SRCC2 0.8341 0.8501 0.8655
  1. Spearman's rank correlation coefficient of RPKM, MART, PDEGEM with the true transcript abundance measured by transcript concentration in the experiment [25]. We compared four different methods using a synthetic RNA-Seq dataset with 90 isoforms. The number in bold indicates the highest R2 among three methods for the dataset.
  2. 1RPKM has no R2.
  3. 2 Spearman's rank correlation coefficient.
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BMC Medical Genomics

ISSN: 1755-8794

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