Table 2

Agreement between technical replicates and biological replicates for RPKM measured on FB 5.4 exons (n = 60,277).

Experiment

Comparison

Number of exons in common

Exons detected in only one of the two replicates

Kappa for detection

Detected in one replicate, RPKM > 20 in the other replicate

Kappa on a 3 level scale

Kappa on a 9 level log scale

Number of exons where disagreement is greater than 2 logs

Number of exons that disagree 1 log or more


c167

TR1-TR2

36602

5154

0.812

0

0.854

0.886

128

11596


c167

TR1-TR3

36937

5236

0.808

0

0.853

0.888

119

11395


c167

TR1-TR4

37102

5153

0.810

0

0.854

0.887

111

11562


c167

TR1-TR5

37037

5202

0.808

0

0.853

0.885

112

11686


c167

TR2-TR3

36974

5208

0.808

0

0.855

0.889

104

11285


c167

TR2-TR4

37102

5199

0.808

1

0.853

0.886

95

11600


c167

TR2-TR5

37039

5244

0.807

2

0.851

0.884

102

11779


c167

TR3-TR4

37514

5127

0.809

0

0.857

0.892

76

11026


c167

TR3-TR5

37470

5134

0.809

0

0.856

0.891

98

11051


c167

TR4-TR5

37626

5069

0.811

0

0.858

0.893

58

10869


D. mel..

BR2:TR1-TR2

46123

4941

0.738

67

0.779

0.801

204

14972


D. mel..

BR3:TR1-TR2

45942

4716

0.754

46

0.783

0.798

297

15122


D. mel..

BR4:TR1-TR2

45310

4652

0.767

110

0.814

0.848

105

12206


D. sim.

BR1:TR1-TR2

43614

4458

0.797

343

0.834

0.861

317

14590


D. sim.

BR2:TR1-TR2

49941

3676

0.748

0

0.864

0.909

2

8530


D. sim.

BR3:TR1-TR2

49983

3690

0.746

2

0.861

0.905

6

8648


D. mel..

BR2-BR3

45675

5045

0.739

62

0.803

0.843

58

11266


D. mel..

BR2-BR3

45715

5003

0.741

70

0.776

0.796

289

15304


D. mel..

BR2-BR3

46274

4806

0.744

41

0.779

0.797

271

15149


D. mel..

BR2-BR3

46381

4630

0.753

50

0.815

0.852

70

11775


D. mel..

BR3-BR4

45612

4967

0.748

84

0.774

0.787

444

15891


D. mel..

BR3-BR4

45387

4869

0.750

96

0.773

0.785

446

15938


D. mel..

BR3-BR4

45723

4685

0.759

88

0.803

0.831

176

13434


'D. mel..

BR3-BR4

45450

4879

0.752

108

0.797

0.828

201

13718


D. mel..

BR2-BR4

45459

5008

0.744

113

0.774

0.789

405

15754


D. mel..

BR2-BR4

45200

5174

0.739

108

0.771

0.790

401

15808


D. mel..

BR2-BR4

46067

4751

0.750

75

0.801

0.834

154

13104


D. mel..

BR2-BR4

45846

4841

0.749

89

0.799

0.832

152

13312


D. sim.

BR1-BR2

45442

6695

0.645

362

0.640

0.654

4936

29729


D. sim.

BR1-BR2

45440

6855

0.635

346

0.640

0.658

4687

29659


D. sim.

BR1-BR2

45341

6827

0.639

395

0.639

0.654

4909

29709


D. sim.

BR1-BR2

45375

6915

0.633

402

0.640

0.658

4665

29629


D. sim.

BR1-BR3

45444

6824

0.637

326

0.640

0.655

4835

29452


D. sim.

BR1-BR3

45464

6772

0.640

346

0.642

0.655

4814

29486


D. sim.

BR1-BR3

45368

6906

0.634

355

0.640

0.656

4761

29404


D. sim.

BR1-BR3

45368

6894

0.635

343

0.640

0.656

4704

29438


D. sim.

BR2-BR3

49844

3847

0.737

1

0.828

0.865

104

12328


D. sim.

BR2-BR3

49835

3853

0.737

0

0.830

0.865

98

12327


D. sim.

BR2-BR3

49955

3781

0.739

2

0.829

0.865

113

12376


D. sim.

BR2-BR3

49891

3897

0.731

0

0.828

0.865

95

12413


All technical replicates were compared between biological replicates. For example, BR1 TR1 was compared to BR2 TR1, BR2 TR2, and BR2 TR3 for all possible pairwise comparisons. Agreement in whether exons are detected (defined as at least one read mapping to the exon), detected at a low level (0 < RPKM < 20), and detected at a high level (RPKM > 20) and agreement on a 9 level ordinal scale as follows: RPKM less than 10, 20, 40, 80, 160, 320, 1000 and greater than 1000. Agreement was measured using a kappa coefficient. The number of exons where disagreement is greater than 2 logs and greater than one log are also given. Agreement for common contigs is in Additional file 9, Supplementary Table S3

McIntyre et al. BMC Genomics 2011 12:293   doi:10.1186/1471-2164-12-293

Open Data