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Table 4 Comparison of the differential expression analysis between HG-U133Plus2 and Hugene 1.0 ST arrays preprocessed with affyILM and several summarization procedures

From: From hybridization theory to microarray data analysis: performance evaluation

Summary

Data

Diff. expr.

m1 m9

m2 m8

m3 m7

m4 m6

m1 m6

m4 m9

m1 m4

m6 m9

m1 m5a

m5a m9

m1 m5b

m5b m9

m1 m5c

m5c m9

Average difference

Raw

Student

0.46

0.44

0.37

0.30

0.43

0.42

0.41

0.28

0.47

0.44

0.46

0.43

0.44

0.37

  

Win. t

0.54

0.52

0.46

0.39

0.51

0.52

0.50

0.36

0.55

0.53

0.55

0.52

0.53

0.48

  

Reg. t

0.47

0.43

0.37

0.35

0.46

0.46

0.48

0.29

0.50

0.44

0.48

0.43

0.48

0.42

 

Scaled

Student

0.42

0.42

0.45

0.33

0.43

0.43

0.34

0.32

0.37

0.40

0.40

0.40

0.36

0.37

  

Win. t

0.53

0.53

0.54

0.43

0.52

0.53

0.43

0.40

0.46

0.50

0.50

0.50

0.45

0.49

  

Reg. t

0.46

0.46

0.49

0.39

0.45

0.48

0.39

0.34

0.38

0.42

0.41

0.42

0.39

0.43

Li-Wong MBEI

Raw

Student

0.47

0.40

0.38

0.33

0.45

0.46

0.41

0.32

0.47

0.48

0.47

0.46

0.43

0.38

  

Win. t

0.52

0.49

0.44

0.42

0.50

0.53

0.49

0.38

0.53

0.56

0.53

0.54

0.50

0.50

  

Reg. t

0.46

0.43

0.39

0.41

0.46

0.48

0.47

0.33

0.49

0.51

0.50

0.50

0.47

0.47

 

Scaled

Student

0.38

0.39

0.43

0.35

0.40

0.43

0.32

0.34

0.33

0.41

0.36

0.42

0.32

0.39

  

Win. t

0.49

0.49

0.52

0.44

0.49

0.53

0.40

0.43

0.42

0.51

0.46

0.52

0.43

0.52

  

Reg. t

0.42

0.41

0.47

0.41

0.44

0.48

0.36

0.37

0.38

0.48

0.42

0.48

0.39

0.49

1-Step Tukey-Biweight

Raw

Student

0.52

0.50

0.42

0.36

0.49

0.49

0.50

0.36

0.54

0.54

0.53

0.52

0.52

0.43

  

Win. t

0.57

0.56

0.48

0.44

0.55

0.57

0.57

0.42

0.61

0.61

0.60

0.59

0.58

0.54

  

Reg. t

0.52

0.53

0.44

0.44

0.51

0.53

0.56

0.37

0.57

0.57

0.57

0.56

0.56

0.52

 

Scaled

Student

0.45

0.45

0.48

0.37

0.45

0.47

0.40

0.39

0.41

0.45

0.43

0.46

0.41

0.42

  

Win. t

0.56

0.56

0.58

0.47

0.55

0.58

0.49

0.47

0.50

0.56

0.53

0.57

0.50

0.56

  

Reg. t

0.51

0.50

0.55

0.46

0.51

0.55

0.46

0.43

0.46

0.53

0.50

0.54

0.47

0.54

Median

Raw

Student

0.46

0.45

0.38

0.30

0.43

0.43

0.40

0.29

0.47

0.45

0.46

0.44

0.44

0.37

  

Win. t

0.55

0.53

0.47

0.40

0.52

0.53

0.50

0.37

0.55

0.54

0.55

0.53

0.53

0.49

  

Reg. t

0.49

0.49

0.42

0.39

0.48

0.49

0.48

0.31

0.52

0.49

0.52

0.48

0.49

0.46

 

Scaled

Student

0.43

0.42

0.45

0.34

0.43

0.43

0.34

0.32

0.37

0.41

0.40

0.41

0.36

0.38

  

Win. t

0.54

0.54

0.54

0.43

0.53

0.54

0.42

0.41

0.46

0.51

0.50

0.52

0.45

0.50

  

Reg. t

0.48

0.48

0.51

0.42

0.48

0.50

0.38

0.35

0.41

0.47

0.45

0.48

0.42

0.48

Median-polish

Raw

Student

0.59

0.58

0.47

0.42

0.55

0.57

0.52

0.46

0.62

0.65

0.59

0.61

0.57

0.51

  

Win. t

0.64

0.63

0.52

0.48

0.60

0.62

0.61

0.50

0.66

0.69

0.64

0.66

0.63

0.61

  

Reg. t

0.64

0.64

0.52

0.51

0.61

0.62

0.62

0.51

0.67

0.68

0.64

0.67

0.64

0.61

 

Scaled

Student

0.53

0.54

0.55

0.43

0.53

0.54

0.40

0.45

0.43

0.52

0.46

0.54

0.44

0.49

  

Win. t

0.62

0.63

0.64

0.52

0.61

0.63

0.51

0.55

0.54

0.62

0.58

0.63

0.54

0.62

  

Reg. t

0.62

0.62

0.64

0.55

0.62

0.64

0.53

0.56

0.55

0.64

0.59

0.65

0.55

0.64

  1. We compared the results of the differential expression analysis of the Tissue Mixture Study between HG-U133plus2 and Hugene 1.0 ST arrays, using Student t-test, Regularized t-test and Window t-test. Preprocessing was performed with affyILM. For each combination of summarization/analysis steps (rows), and each comparison of mixtures (columns), Pearson's correlation coefficient has been computed on log10(p-values) between both types of arrays. Underlined characters highlight the top 5 correlation coefficients for each column. The best match table provided by Affymetrix has been used to map probesets between the two platforms. Raw/Scaled labels respectively refers to summarization tests performed with/without a scaling step between arrays.