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Table 3 Comparison of correlations (r) between MAQC2 RNA-Seq data and other platforms.

From: Bias detection and correction in RNA-Sequencing data

Platform1

Platform2

Sample

Log fold changes

Original r

r after GAM Correction

%Relative improvement

RNA-Seq

Taqman

Brain

(0, 0.326]

0.749

0.747

-0.3

   

(0.326, 0.731]

0.664

0.699

5.3

   

(0.731, 2.1]

0.655

0.807

23.2

   

Overall

0.69

0.754

9.3

RNA-Seq

Taqman

UHR

(0, 0.368]

0.778

0.774

-0.5

   

(0.368, 0.753]

0.776

0.79

1.8

   

(0.753, 1.78]

0.704

0.724

2.8

   

Overall

0.748

0.763

2

RNA-Seq

QuantiGene

Brain

(0, 0.3]

0.833

0.823

-1.2

   

(0.3, 0.743]

0.659

0.721

9.4

   

(0.743, 1.69]

0.647

0.738

14.1

   

Overall

0.725

0.766

5.7

RNA-Seq

QuantiGene

UHR

(0, 0.375]

0.832

0.839

0.8

   

(0.375, 0.793]

0.811

0.759

-6.4

   

(0.793, 1.78]

0.632

0.692

9.5

   

Overall

0.771

0.777

0.8

  1. Gene expression levels from Taqman RT-PCR or QuantiGene platforms are compared with RNA-Seq data, before and after bias correction by GAM.