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Table 1 Recall of negative selection heuristics at 80% and 60% of precision.

From: A negative selection heuristic to predict new transcriptional targets

Method

%of Known Positives

Recall (Pr = 80%)

p-value

(corrected)

Recall (Pr = 60%)

p-value (corrected)

NOIT

10

0.179 (± 0.052)

 

0.203 (± 0.053)

 

PSOL

10

0.043 (± 0.020)

2.0 · 10 -5

0.070 (± 0.031)

1.2 · 10 -4

BAGGING

10

0.066 (± 0.027)

7.1 · 10 -4

0.132 (± 0.051)

9.5 · 10-2

ROCCHIO

10

0.036 (± 0.023)

1.1 · 10 -5

0.053 (± 0.032)

2.0 · 10 -5

SPY

10

0.022 (± 0.011)

7.3 · 10 -7

0.038 (± 0.017)

6.4 · 10 -7

PU

10

0.013 (± 0.004)

2.0 · 10 -7

0.038 (± 0.017)

6.4 · 10 -7

NOIT

30

0.252 (± 0.060)

 

0.384 (± 0.059)

 

PSOL

30

0.140 (± 0.039)

5.9 · 10 -3

0.232 (± 0.052)

5.7 · 10 -4

BAGGING

30

0.158 (± 0.047)

3.5 · 10 -2

0.272 (± 0.067)

2.9 · 10 -2

ROCCHIO

30

0.006 (± 0.002)

1.8 · 10 -10

0.010 (± 0.006)

1.2 · 10 -16

SPY

30

0.123 (± 0.036)

1.1 · 10 -3

0.200 (± 0.049)

2.0 · 10 -5

PU

30

0.079 (± 0.024)

3.3 · 10 -6

0.160 (± 0.036)

3.5 · 10 -8

NOIT

50

0.294 (± 0.062)

 

0.446 (± 0.065)

 

PSOL

50

0.240 (± 0.056)

3.6 · 10-1

0.366 (± 0.064)

1.3 · 10-1

BAGGING

50

0.245 (± 0.053)

3.9 · 10-1

0.374 (± 0.069)

1.8 · 10-1

ROCCHIO

50

0.010 (± 0.006)

1.1 · 10 -11

0.017 (± 0.011)

1.3 · 10 -17

SPY

50

0.228 (± 0.062)

2.6 · 10-1

0.336 (± 0.067)

4.0 · 10 -2

PU

50

0.230 (± 0.053)

2.5 · 10-1

0.320 (± 0.056)

9.8 · 10 -3

NOIT

70

0.278 (± 0.064)

 

0.486 (± 0.066)

 

PSOL

70

0.249 (± 0.063)

7.4 · 10-1

0.397 (± 0.071)

1.1 · 10-1

BAGGING

70

0.304 (± 0.059)

7.4 · 10-1

0.433 (± 0.071)

3.7 · 10-1

ROCCHIO

70

0.011 (± 0.006)

1.6 · 10 -10

0.019 (± 0.012)

5.9 · 10 -19

SPY

70

0.233 (± 0.064)

5.0 · 10-1

0.359 (± 0.074)

2.6 · 10 -2

PU

70

0.305 (± 0.066)

7.4 · 10-1

0.435 (± 0.068)

3.7 · 10-1

NOIT

90

0.328 (± 0.066)

 

0.511 (± 0.065)

 

PSOL

90

0.239 (± 0.070)

1.4 · 10-1

0.391 (± 0.081)

4.1 · 10 -2

BAGGING

90

0.352 (± 0.065)

7.5 · 10-1

0.494 (± 0.062)

8.6 · 10-1

ROCCHIO

90

0.011 (± 0.005)

3.7 · 10 -12

0.022 (± 0.013)

4.9 · 10 -20

SPY

90

0.296 (± 0.068)

7.4 · 10-1

0.436 (± 0.071)

1.8 · 10-1

PU

90

0.337 (± 0.067)

1

0.509 (± 0.064)

1

  1. The table shows, at different percentage of known positives, the average Recalls of negative at 80% and 60% of precision (lower and upper 95% confidence intervals is shown in parentheses). The p-value column (corrected with Benjamini & Hochberg) is the outcome of a t-test performed to check whether the recall of NOIT is greater than the recall of another negative selection method. A p-value shown in boldface means that the statistical significance of the test is less than 0.05.
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BMC Bioinformatics

ISSN: 1471-2105

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