Table 3

Cluster-based prediction of phenotypic resistance relative to controls.

With all data

RTV

NFV

ATV

APV

IDV

LPV

SQV

TPV

DRV

CTL1 (Random)

% correct

35

36

29

21

22

26

29

31

29

CTL1 (Random)

RMSE

1.34

1.13

1.21

1.2

1.05

1.01

1.26

0.98

0.76

CTL2 (Average)

% correct

46

43

62

60

62

56

57

47

34

CTL2 (Average)

RMSE

0.60

0.54

0.36

0.34

0.26

0.28

0.41

0.67

0.67

Cluster-based

% correct

81

75

74

70

63

67

65

50

67

Cluster-based

RMSE

0.35

0.34

0.38

0.33

0.29

0.25

0.50

0.71

0.29

Without nonresistant clusters

RTV

NFV

ATV

APV

IDV

LPV

SQV

TPV

DRV

CTL1 (Random)

% correct

78

66

45

27

22

29

34

18

29

CTL1 (Random)

RMSE

0.54

0.68

0.84

0.97

0.86

0.83

1.06

1.00

0.74

CTL2 (Average)

% correct

28

32

49

51

52

43

46

28

11

CTL2 (Average)

RMSE

0.74

0.64

0.45

0.41

0.32

0.34

0.51

0.84

0.84

Cluster-based

% correct

89

82

73

62

55

58

60

34

56

Cluster-based

RMSE

0.26

0.23

0.38

0.40

0.36

0.31

0.62

0.89

0.36

Percent of viruses whose resistance score toward each drug was correctly classified ("% correct"), as well as the RMS error (in scaled resistance units) over all sequences of the phenotypic difference between predicted and actual phenotype ("RMSE") using the two controls described in the text ("CTL1 (Random)" and "CTL2 (Average)" and the cluster-based prediction. The top panel presents results using all 398 sequences, and the bottom panel shows results after removing the two clusters showing little or no phenotypic resistance to any drug.

Doherty et al. BMC Bioinformatics 2011 12:477   doi:10.1186/1471-2105-12-477