
Invariant feature (AD)

Invariant feature (MBEV)

Invariant set

Global scaling


(a) Mean

3.55

2.45

1.59

3.37

Median

2.09

1.46

1.30

2.12

Max

429.01

667.16

71.63

848.28

(b) Mean FC
    
F

15.05

9.69

3.06

10.28

KW

18.48

12.24

3.35

12.21

SAM

21.91

13.75

3.63

13.08

Median FC
    
F

5.77

2.97

2.08

3.89

KW

7.89

3.63

2.25

4.77

SAM

9.20

4.11

2.41

4.92

(c) Mean

428.71

750.20

324.17

384.47

Median

85.52

259.83

122.04

102.37

Max

25141.89

24616.80

28650.70

24794.22

(d) Mean difference
    
F

2248.04

3346.51

1427.59

1784.93

KW

2545.81

3881.37

1655.16

2044.61

SAM

3157.21

4451.51

1827.97

2216.36

Median difference
    
F

1116.52

1954.57

664.49

954.38

KW

1328.38

2444.28

815.85

1138.39

SAM

1865.47

2927.57

952.92

1248.04

 (a) Mean, median, and maximum fold changes (FC) of all genes on the two array types normalized with different methods. AD, average difference; MBEV, modelbased expression values. The averages are given across all genes of the ratio between the maximum and the minimum value across the five different conditions, calculated after averaging replicate arrays. (b) Mean and median fold changes (FC) of genes detected as differentially expressed with 99% confidence by all possible combinations of normalization and statistical analysis algorithms, calculated as in (a). F, Fstatistics; KW, KruskalWallis; significance analysis of microarrays (SAM), (c) Mean, median, and maximum signal differences of all genes on the two array types normalized with different methods, calculated by analogy with the ratios in (a). (d) Mean and median signal differences of genes detected as differentially expressed with 99% confidence by all possible combinations of normalization and statistical analysis algorithms, calculated as in (c).