Skip to main content

Table 3 Concordance between platforms using statistically significant expression ratios at p-value < 0.05 and at 1.5 and 2-fold threshold levels.1

From: Three microarray platforms: an analysis of their concordance in profiling gene expression

 

No threshold

1.5-fold

2-fold

 

GEM2 vs. Operon

GEM2 vs. U133A

Operon vs. U133A

GEM2 vs. Operon

GEM2 vs. U133A

Operon vs. U133A

GEM2 vs. Operon

GEM2 vs. U133A

Operon vs. U133A

Number of comparisons 2

Jurkat

1471

1678

1740

1096

1088

1220

588

614

749

L428

651

1394

750

580

1051

632

430

678

469

SUDHL

1400

1527

1707

1081

1177

1277

698

741

831

OCI-Ly3

1484

1834

1698

1285

1428

1333

814

900

903

LNCaP

1167

1170

2062

737

751

1252

369

404

696

MCF10A

1555

1429

1880

899

812

1118

405

409

559

Percent of concordance

Jurkat

97%

96%

98%

98%

99%

100%

99%

99%

100%

L428

96%

96%

98%

98%

98%

99%

99%

99%

100%

SUDHL

95%

97%

98%

97%

98%

99%

99%

99%

100%

OCI-Ly3

94%

96%

96%

95%

98%

98%

98%

99%

99%

LNCaP

93%

95%

96%

97%

98%

99%

99%

100%

100%

MCF10A

94%

95%

96%

98%

98%

99%

99%

99%

100%

Total number of comparisons

 

7728

9032

9837

5678

6307

6832

3304

3746

4207

Total number of concordances

 

7334

8650

9540

5509

6191

6755

3257

3719

4190

Percent agreement

 

94.9%

95.8%

97.0%

97.0%

98.2%

98.9%

98.6%

99.3%

99.6%

Percent of data used 3

 

54.0%

57.5%

60.4%

39.7%

40.2%

42.0%

23.1%

23.9%

25.8%

  1. 1GEM2: Incyte GEM2 arrays; Operon: Operon V2 arrays; U133A: Affymetrix Human Genome U 133A GeneChip arrays.
  2. 2Comparisons between two platforms were done only when the expressions of both platforms met the p-value and threshold criteria.
  3. 3Fraction of common expressions between two platforms to the total number of expressions found at p < 0.05 in both platforms.