Skip to main content

Table 3 Comparison of preprocessing data sets by GC-RMA or MAS5 algorithms on the significance of fixed factors as revealed by LMMA analyses

From: Infection and genotype remodel the entire soybean transcriptome

FDR (TST)a

Fixed factorb

Number significant genesc

Number matchesd

Percentage matchese

  

GC-RMA

MAS5

  

0.05

Genotype

27,156

26,651

25,896

97.2

 

Treatment

27,732

27,585

27,099

98.2

 

Genotype × Treatment

26,500

25,932

24,977

96.3

 

Time

9,960

9,038

6,961

77

0.01

Genotype

25,923

25,162

24,024

95.5

 

Treatment

27,139

26,864

26,079

97.1

 

Genotype × Treatment

24,669

23,643

22,327

94.4

 

Time

4,453

3,655

2,941

80.5

0.001

Genotype

24,191

23,161

21,780

94

 

Treatment

26,351

25,962

24,873

95.8

 

Genotype × Treatment

22,381

20,924

19,507

93.2

 

Time

2,025

1,551

1,348

86.9

0.0001

Genotype

22,611

21,270

19,800

93.1

 

Treatment

25,560

25,126

23,817

94.8

 

Genotype × Treatment

20,293

18,691

17,256

92.3

 

Time

1,173

857

768

89.6

  1. aFalse discovery rate (FDR) was controlled using the two-stage linear step-up method (TST). bThe fixed factors used in the LMMA model included genotype (V71-370, Sloan and VPRIL9), treatment (Upper, Lower, and Mock), time (9 am, 10:30 am, and 12 pm), and the genotype × treatment interaction. cNumber of significant genes for a factor was determined by LMMA analysis with FDR control. dThe number of genes called significant following GC-RMA and following MAS5 pre-processing. eThe number of matches as a percentage of the minimum of the number of significant genes called following GC-RMA or MAS5 preprocessing.