Table 2

Correlation of quantification method predictions with MAQC qRT-PCR values

SRA ID

Read type

Sample

RSEM

IsoEM

IsoEM (C)

Cufflinks

Cufflinks (C)

rQuant


SRX016366

SE

HBR

0.69

0.68

0.68

0.71

0.79

0.72

SRX003926

SE

HBR

0.68

0.67

0.67

0.7

0.73

0.71

SRX018974

PE

HBR

0.69

0.69

0.69

0.69

0.78

NA

SRX016368

SE

UHR

0.71

0.71

0.72

0.72

0.77

0.72

SRX016369

SE

UHR

0.73

0.74

0.74

0.73

0.76

0.74

SRX016370

SE

UHR

0.74

0.75

0.75

0.74

0.77

0.75

SRX016371

SE

UHR

0.74

0.75

0.75

0.74

0.77

0.75

SRX016372

SE

UHR

0.75

0.75

0.75

0.74

0.77

0.76

SRX003927

SE

UHR

0.72

0.71

0.72

0.71

0.74

0.72


Correlation values (Pearson r2 of log-transformed abundance values) were computed between the predictions of four methods and "gold-standard" values from qRT-PCR for nine different RNA-Seq data sets. IsoEM and Cufflinks were run with (C) and without their bias correction modes.

Li and Dewey BMC Bioinformatics 2011 12:323   doi:10.1186/1471-2105-12-323

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