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Table 1 Computed relative mRNA proportions. Computed relative mRNA proportions p M (macrophages) and p F (fibroblasts) for patients 1–6 calculated for different chip evaluation methods. The proportion of non-adherent cells is p N = 1 - p M - p F . The primed 1 in 'patient 1' (RA)' indicates the use of the second tissue chip replicate for patient 1. Additional stepwise local regression normalization is indicated by lr. The proportions are given in percent. Probe set summaries: MAS-S: Microarray Suite 5.0 signal algorithm, RMA: Robust Multiarray Analysis, MBEI: Model Based Expression Index, GP: GenePublisher (not available for HG-U95A chips, patient 1), the R implementation of MBEI was used with the same settings as in GP. Normalization methods: t: trimmed mean, clr: cyclic local regression, q: quantile normalization, c: centralization.

From: Robust computational reconstitution – a new method for the comparative analysis of gene expression in tissues and isolated cell fractions

chip evaluation method

patient 1' (RA)

patient 2 (RA)

patient 3 (RA)

patient 4 (QA)

patient 5 (QA)

patient 6 (QA)

  

lr

 

lr

 

lr

 

lr

 

lr

 

lr

 

M

F

M

F

M

F

M

F

M

F

M

F

M

F

M

F

M

F

M

F

M

F

M

F

MAS-S t

29

16

29

19

82

9

79

6

64

27

64

29

57

24

57

27

72

21

69

20

86

13

81

19

MAS-S t clr

32

18

29

22

90

10

86

5

66

30

64

33

65

25

64

30

74

21

68

25

78

22

74

26

MAS-S t q

31

14

24

22

92

8

93

6

69

30

63

34

66

23

63

30

87

07

71

22

71

29

67

33

MAS-S t c

31

15

29

17

80

5

80

6

59

31

65

30

71

16

66

21

80

13

80

11

96

2

80

20

RMA

44

24

28

31

95

5

82

16

49

42

45

45

60

26

46

36

94

0

85

8

96

0

100

0

MBEI

44

15

42

19

91

5

76

2

38

52

45

49

66

2

57

10

98

0

92

5

100

0

99

1

MBEI-GP

--

--

--

--

98

1

88

9

26

62

43

55

57

5

38

18

92

0

94

0

100

0

100

0