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Table 4 Validation and real-time PCR measures computed with three different DNA extraction methods on three matrices

From: Testing the interaction between analytical modules: an example with Roundup Ready®soybean line GTS 40-3-2

Validation/efficiency measures

(and fuzzy-based modules and indicator)

DNA extraction method

  

CTAB

Wizard

Dellaporta

CRM 1%

Basic measures

Average bias (B, %)

22.3

10.5

14.0

 

Relative standard deviation repeatability (RSD r , %)

13.8

34.6

9.6

 

Reference gene efficiency (E 1 , %)

99.4

99.8

99.8

 

Target gene efficiency (E 2 , %)

99.7

99.5

99.2

Fuzzy-based aggregated measures

Accuracy

0.4271

0.5000

0.0000

 

Efficiency

0.0000

0.0000

0.0000

 

Indicator

0.2736

0.3750

0.0000

Feed

Basic measures

Average bias (B, %)

0.8

23.5

1.6

 

Relative standard deviation repeatability (RSD r , %)

20.5

-*

11.8

 

Reference gene efficiency (E 1 , %)

99.4

99.8

99.8

 

Target gene efficiency (E 2 , %)

99.0

98.5

99.2

Fuzzy-based aggregated measures

Accuracy

0.0011

-*

0.0000

 

Efficiency

0.0000

0.0000

0.0000

 

Indicator

~0.0000

-*

0.0000

Biscuit

Basic measures

Average bias (B, %)

12.3

87.5

29.9

 

Relative standard deviation repeatability (RSD r , %)

14.8

37.7

14.0

 

Reference gene efficiency (E 1 , %)

99.7

99.9

99.8

 

Target gene efficiency (E 2 , %)

99.7

99.8

99.2

Fuzzy-based aggregated measures

Accuracy

0.0000

1.0000

0.5000

 

Efficiency

0.0000

0.0000

0.0000

 

Indicator

0.0000

0.7500

0.3750

  1. - Not including data violating DNA quality acceptance from inhibition tests.
  2. - Estimated robust means are: feed, 0.87%; biscuit, 1.84%. Fuzzy logic is used to computed aggregated measures of B and RSD r (Accuracy), E 1 and E 2 (Efficiency), and an overall indicator
  3. * Impossible to calculate repeatability and derived measures for lack of replicates.