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Table 5 Consistency between transcript abundance estimated by different methods and gold standards in Dataset 3.

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

Sample N1 RPKM PL2 MART PDEGEM
SRX0005713 4857 0.474 0.474 0.471 0.483
SRX0006043 4880 0.460 0.458 0.460 0.477
SRX0006054 5309 0.527 0.527 0.530 0.557
SRX0006064 5293 0.442 0.411 0.452 0.471
  1. Spearman's rank correlation coefficient of RPKM, Poisson-Linear model, MART, PDEGEM with the "true" gene expression measured by microarray in Dataset 3.
  2. 1 Number of transcripts used to calculate the correlation coefficients.
  3. 2 PL: the Poisson-Linear model.
  4. 3 Illumina sequencing of Human liver transcripts.
  5. 4 Illumina sequencing of Human kidney transcripts.
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BMC Medical Genomics

ISSN: 1755-8794

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