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Table 1 Affycomp III results

From: Iterative rank-order normalization of gene expression microarray data

  

HG-U95a

HG-U133a

Metric #

Metric Name

MAS5-apt

IRON

RMA-apt

dChip

MAS5-apt

IRON

RMA-apt

dChip

1

Median SD

0.59

0.20

0.11

0.32

0.29

0.14

0.07

0.20

2

null log-fc IQR

0.84

0.33

0.19

0.38

0.47

0.24

0.13

0.26

3

null log-fc 99.9%

4.46

1.59

0.57

10.83

4.01

1.42

0.40

9.61

4

Signal detect R2

0.86

0.82

0.80

0.61

0.91

0.90

0.90

0.65

5

Signal detect slope

0.71

0.67

0.63

0.91

0.77

0.69

0.68

0.98

6

low.slope

0.69

0.44

0.35

1.17

0.65

0.41

0.31

1.29

7

med.slope

0.81

0.82

0.76

0.87

0.71

0.68

0.71

0.75

8

high.slope

0.45

0.50

0.47

0.34

0.77

0.83

0.80

0.69

9

Obs-intended-fc slope

0.69

0.66

0.61

0.87

0.77

0.69

0.68

0.99

10

Obs-(low)int-fc slope

0.65

0.44

0.36

1.68

0.64

0.40

0.31

1.17

11

low AUC

0.00

0.03

0.40

0.04

0.00

0.08

0.51

0.08

12

med AUC

0.00

0.03

0.87

0.00

0.00

0.10

0.88

0.00

13

high AUC

0.00

0.00

0.46

0.00

0.00

0.13

0.93

0.00

14

weighted avg AUC

0.00

0.03

0.52

0.03

0.00

0.08

0.60

0.06

  1. IRON generally performs in-between MAS5 and RMA, as expected, due to the mix of RMA background subtraction (RMA) and Tukey’s Biweight probeset summarization (MAS5). Metrics 1-10 are closer to RMA due to the use of RMA background subtraction, while metrics 11-14 are closer to MAS5 due to the use of Tukey’s Biweight probeset summarization.