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

BMC Medical Genomics

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

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

Spearman's rank correlation coefficient of RPKM, Poisson-Linear model, MART, PDEGEM with the "true" gene expression measured by microarray in Dataset 3.
¹ Number of transcripts used to calculate the correlation coefficients.
² PL: the Poisson-Linear model.
³ Illumina sequencing of Human liver transcripts.
⁴ Illumina sequencing of Human kidney transcripts.

ISSN: 1755-8794