Table 4

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

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 (E₁, %)

99.4

99.8

99.8

Target gene efficiency (E₂, %)

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 (E₁, %)

99.4

99.8

99.8

Target gene efficiency (E₂, %)

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 (E₁, %)

99.7

99.9

99.8

Target gene efficiency (E₂, %)

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

- Not including data violating DNA quality acceptance from inhibition tests.

- Estimated robust means are: feed, 0.87%; biscuit, 1.84%. Fuzzy logic is used to computed aggregated measures of B and RSD_r (Accuracy), E₁ and E₂ (Efficiency), and an overall indicator

* Impossible to calculate repeatability and derived measures for lack of replicates.

Bellocchi et al. BMC Biotechnology 2010 10:55   doi:10.1186/1472-6750-10-55