N–P

Find reference information on document elements of the Biological Assay Package, letters N to P.

n Sigma

Enter the factor to be multiplied with the standard deviation.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:double 1...1 required none

Context:

/Quantitative response assay/Analysis/Data selection schemes/Data selection scheme/choice/Standard deviation test/

Name

Enter a name for this column.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 0...1 required none

/Basic bioassay protocol/Reportable values/Document reference/

/Combination of independent assay results/Setup/Potency data/Column: Document reference/

/Equivalence margin development (Quantitative response assays)/Data table/Column: Document reference/

/Quantitative response assay/Setup/Observation data/Column: Document reference/

Name

Enter a name for the Control line.

The name is used to report test results, data values, and estimates related to this Control line. It is also displayed in the Observation group ID column of the Observations editor.

Examples:

'Positive control', 'Negative control', 'Blank'

Tip: We recommend to use assay element names that are unique within the assay document. But this is not required. Assay elements are internally identified by their unique Observation group ID.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 required none

/Basic bioassay protocol/choice/Mode: Assay element/Control line/

/Quantitative response assay/Setup/Assay elements/Control line/

Name

Enter a name for the Control sample.

The name is used to report test results, data values, and estimates related to this Control sample. It is also displayed in the Observation group ID column of the Observations editor.

Examples:

'Assay control', 'Control 3', 'Ctr'

Tip: We recommend to use assay element names that are unique within the assay document. But this is not required. Assay elements are internally identified by their unique Observation group ID.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 required none

/Basic bioassay protocol/choice/Mode: Assay element/Control sample/

/Quantitative response assay/Setup/Assay elements/Control sample/

Name

Enter a name for the Data selection scheme.

Note: We recommend to use unique names. But this is not required.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 required none

Context:

/Quantitative response assay/Analysis/Data selection schemes/Data selection scheme/

Name

Enter a name for this document.

Note: Documents are usually identified by name. We therefore recommend to use unique document names. But this is not required.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 required none

/Basic bioassay protocol/

/Combination of independent assay results/

/Equivalence margin development (Quantitative response assays)/

/Quantitative response assay/

/Test system definition (Quantitative response assay)/

Name

Enter a name for the group.

Note: With document aggregation, the name needs to match the name of the group that is assigned to the Test sample in the referenced assay document.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 optional none

Context:

/Combination of independent assay results/Documentation/Groups/Group/

Name

Enter a name for the Preparation scheme.

Note: Preparation scheme names are required to be unique within assays.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 required none

Context:

/Quantitative response assay/Setup/Preparation schemes/Preparation scheme/

Name

Enter a name for this column.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 required none

Context:

/Quantitative response assay/Setup/Observation data/Column: Response value/

Name

Enter a name for the Standard sample.

The name is used to report test results, data values, and estimates related to this Standard sample. It is also displayed in the Observation group ID column of the Observations editor.

Examples:

'Standard', 'Std', 'Reference standard'

Tip: We recommend to use assay element names that are unique within the assay document. But this is not required. Assay elements are internally identified by their unique Observation group ID.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 required none

/Basic bioassay protocol/choice/Mode: Assay element/Standard sample/

/Quantitative response assay/Setup/Assay elements/Standard sample/

Name

Enter a name for the Test sample.

The name is used to report test results, data values, and estimates related to this Test sample. It is also displayed in the Observation group ID column of the Observations editor.

Examples:

'Preparation 1', 'Unknown 3', 'Test 2'

Tip: We recommend to use assay element names that are unique within the assay document. But this is not required. Assay elements are internally identified by their unique Observation group ID.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 required none

/Basic bioassay protocol/choice/Mode: Assay element/Test sample/

/Quantitative response assay/Setup/Assay elements/Test sample/

Name

Enter a name for the test strategy.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 required none

Context:

/Equivalence margin development (Quantitative response assays)/Test strategies/Strategy/

No adjustment

Performs analysis without response adjustment.

This element has the following attributes:

Data type Multiplicity Usage Default value
Empty 1...1 required none

Context:

/Quantitative response assay/Analysis/Response data processing/choice/Adjustment/choice/

No normalization

Performs analysis without response normalization.

This element has the following attributes:

Data type Multiplicity Usage Default value
Empty 1...1 required none

Context:

/Quantitative response assay/Analysis/Response data processing/choice/Normalization/choice/

No. of dilution factor

Enter the (pre)dilution step for which the intermediate predilution is to be calculated.

  • Let d_1, d_2, …, d_n be the (pre)dilution factors defined for a Test/Control sample, let i be the (pre)dilution step, and let P be the stock solution potency. The predilution potency for this Test/Control sample is then p_t = P/(d_1*…*d_i).
  • Let d_1, d_2, …, d_n be the (pre)dilution factors defined for the Standard sample, let i be the (pre)dilution step, and let P be the assigned potency. The predilution potency for the Test sample is then p_s = P/(d_1*…*d_i).

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:nonNegativeInteger 1...1 required none

Context:

/Quantitative response assay/Analysis/Suitability tests/Assay suitability tests/choice/Test: Potency of intermediate dilution/

/Quantitative response assay/Analysis/Suitability tests/Sample suitability tests/choice/Test: Potency of intermediate dilution/

/Test system definition (Quantitative response assay)/Suitability tests/Assay suitability tests/choice/Test: Potency of intermediate dilution/

/Test system definition (Quantitative response assay)/Suitability tests/Sample suitability tests/choice/Test: Potency of intermediate dilution/

No outlier detection

Performs no outlier detection for assay elements (samples) that reference this Data selection scheme. Select a different option from the drop-down list if you require outlier detection.

This element has the following attributes:

Data type Multiplicity Usage Default value
Empty 1...1 required none

Context:

/Quantitative response assay/Analysis/Data selection schemes/Data selection scheme/choice/

No transformation

Performs analysis without response transformation.

This element has the following attributes:

Data type Multiplicity Usage Default value
Empty 1...1 required none

Context:

/Quantitative response assay/Analysis/Response data processing/choice/Transformation/choice/

Normalization

Normalize your response values by Fixed value, Control line, or Block-based by Control line.

Example: Use this feature to divide by the mean absorbance of maximum binding wells.

Expand the node to add or view information.

This element has the following attributes:

Data type Multiplicity Usage Default value
Node 0...1 optional none

Context:

/Quantitative response assay/Analysis/Response data processing/choice/

Number of positions

Sets the number of positions available for this position factor.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:positiveInteger 1...1 required none

Context:

/Quantitative response assay/Setup/Observation data/Column: Position factor/

Number of replicates

Enter the number of Quantitative response assays to be generated.

Note: If you generate assay replicates, increase the number of replicates, and generate again, only the difference between the previous and current number of replicates is generated.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:integer 1...1 required none

Context:

/Basic bioassay protocol/choice/Mode: Assay replicate/

Number of replicates

Enter the Number of replicates to be generated for this assay element.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:integer 1...1 required none

Context:

/Basic bioassay protocol/choice/Mode: Assay element/Test sample/

/Basic bioassay protocol/choice/Mode: Assay element/Control sample/

Number of signatures

Enter a number to specify how many signatures this document requires.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:integer 0...1 optional none

/Combination of independent assay results/Analysis/Suitability tests/choice/Test: Signature status/

/Quantitative response assay/Analysis/Suitability tests/Document suitability tests/Signature state/

/Test system definition (Quantitative response assay)/Suitability tests/Document suitability tests/Signature state/

Number of steps

Enter a number to specify how many dose steps this sequence requires.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:positiveInteger 1...1 required none

Context:

/Quantitative response assay/Setup/Preparation schemes/Preparation scheme/choice/Geometric sequence/

Observation data

This section allows you to modify the data table that displays observation data in the Observations editor.

Expand the node to add or view information.

This element has the following attributes:

Data type Multiplicity Usage Default value
Node 1...1 required none

Context:

/Quantitative response assay/Setup/

Observation group ID

Displays the Observation group ID. Observation group IDs are natural numbers (zero not included).

When you create an assay element, a unique Observation group ID is automatically assigned. In the Observation group column of the Observations editor, the Observation group ID is displayed in square brackets. Since Observation group IDs are required to be unique within assays, we do not recommend to change them manually.

Important: If you manually change the Observation group ID in the definition of an assay element, this does not change the Observation group IDs of observations that may be assigned to this assay element.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:positiveInteger 1...1 required none

Context:

/Quantitative response assay/Setup/Assay elements/Standard sample/

/Quantitative response assay/Setup/Assay elements/Test sample/

/Quantitative response assay/Setup/Assay elements/Control sample/

/Quantitative response assay/Setup/Assay elements/Control line/

Observation group ID

Enter the ID that signifies the observation group you need to connect this assay element to the proper data. Observation group IDs are natural numbers (zero not included).

Important: The observation group ID you enter here must match the observation group ID that occurs in the template you apply to generate the assay replicate.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:positiveInteger 1...1 required none

Context:

/Basic bioassay protocol/choice/Mode: Assay element/Standard sample/

/Basic bioassay protocol/choice/Mode: Assay element/Test sample/

/Basic bioassay protocol/choice/Mode: Assay element/Control sample/

/Basic bioassay protocol/choice/Mode: Assay element/Control line/

Observation source

Select how you want to obtain observation data. The following options are available:

  • User input: Enter data manually.
  • Aggregation: Specify document references to aggregate data from documents.
  • Import: Not supported.
Note: With document aggregation, you can only use Test samples as data source.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 required none

Context:

/Equivalence margin development (Quantitative response assays)/Data table/

Observation source

The observation source allows you to select how you want to obtain observation data. The Basics bioassay protocol documents type aggregates data from referenced documents. Therefore, the observation source is set to Aggregation and cannot be changed.

  • User input: Enter data manually.
  • Aggregation: Specify document references to aggregate data from documents.
  • Import: Not supported.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 required none

Context:

/Basic bioassay protocol/Reportable values/

Observation source

Select how you want to obtain observation data. The following options are available from the drop-down list:

  • User input: Enter data manually.
  • Aggregation: Specify document references to aggregate data from documents.
  • Import: Not supported.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 required none

/Combination of independent assay results/Setup/Potency data/

/Quantitative response assay/Setup/Observation data/

Operational sequence

Select whether outlier testing is to be performed Before response data processing or After response data processing.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 required none

Context:

/Quantitative response assay/Analysis/Data selection schemes/Data selection scheme/choice/Dixon test/

/Quantitative response assay/Analysis/Data selection schemes/Data selection scheme/choice/Grubbs test/

/Quantitative response assay/Analysis/Data selection schemes/Data selection scheme/choice/Standard deviation test/

Operator

This section allows you to provide information on an operator. Expand the node to add or view information.

To add an Operator name or reference: Select the required option from the drop-down list, and enter the name or reference.

To assign a role to the operator: Add the Role element from the Creatable elements pane, and enter the required role.

This element has the following attributes:

Data type Multiplicity Usage Default value
Node 0...1 optional none

/Basic bioassay protocol/Documentation/

/Combination of independent assay results/Documentation/

Data type Multiplicity Usage Default value
Node 0...unbounded optional none

/Combination of independent assay results/Documentation/

/Quantitative response assay/Documentation/

Operator name

Enter the name of the operator.

Tip: You can enter a reference to an operator document instead. Select the Operator reference option from the drop-down list.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 required none

/Basic bioassay protocol/Documentation/Operator/choice/

/Combination of independent assay results/Documentation/Operator/choice/

/Quantitative response assay/Documentation/Operator/choice/

Operator reference

Select an operator document.

Tip: You can enter an operator name instead. Select the Operator name option from the drop-down list.

This element has the following attributes:

Data type Multiplicity Usage Default value
Node 1...1 required none

/Basic bioassay protocol/Documentation/Operator/choice/

/Combination of independent assay results/Documentation/Operator/choice/

/Quantitative response assay/Documentation/Operator/choice/

Optimization off

Does not use the configuration optimizer to analyze assay elements that reference this Data selection scheme.

Select the Optimization on option from the drop-down list if you want to use the configuration optimizer.

Note: If you combine configuration optimization with simultaneous regression, you create a very large number of configurations. Your system may not be able to calculate all configurations in a timely manner.

This element has the following attributes:

Data type Multiplicity Usage Default value
Empty 1...1 required none

Context:

/Quantitative response assay/Analysis/Data selection schemes/Data selection scheme/choice/

Optimization on

Uses the configuration optimizer to analyze assay elements that reference this Data selection scheme. Expand the node to add or view information.

Note: Configuration optimization is only supported for the linear parallel-line model.

Select the Optimization off option from the drop-down list if you do not want to use the configuration optimizer.

Note: If you combine configuration optimization with simultaneous regression, you create a very large number of configurations. Your system may not be able to calculate all configurations in a timely manner.

This element has the following attributes:

Data type Multiplicity Usage Default value
Node 1...1 required none

Context:

/Quantitative response assay/Analysis/Data selection schemes/Data selection scheme/choice/

Outlier processing

Select how detected outliers are to be processed.

The following options are available from the drop-down list:

  • Remove outlier: Outlying response values are excluded from regression.
  • Remove outlier step: All response values that belong to the step and assay element combinations where outliers occur are excluded from regression.
  • Replace outlier: Outlying response values are replaced by the arithmetic mean of the valid response values of the corresponding step and assay element combination.
  • Mark outlier: Outlying response values are included in regression, but they are marked as outliers in plots and reports.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 required none

Context:

/Quantitative response assay/Analysis/Data selection schemes/

p

Enter the significance level (alpha) for the p-value of the test. A common value is 0.05.

Note: The test evaluation is based on comparing p-values, which are calculated from a test statistic, to the significance level you enter. This is equivalent to comparing test statistics to critical values.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:double 1...1 required none

/Combination of independent assay results/Analysis/Suitability tests/choice/Test: Homogeneity/choice/

/Quantitative response assay/Analysis/Suitability tests/Assay suitability tests/choice/F-test (hypothesis test)/choice/

/Quantitative response assay/Analysis/Suitability tests/Sample suitability tests/choice/F-test (hypothesis test)/choice/

/Test system definition (Quantitative response assay)/Suitability tests/Assay suitability tests/choice/F-test (hypothesis test)/choice/

/Test system definition (Quantitative response assay)/Suitability tests/Sample suitability tests/choice/F-test (hypothesis test)/choice/

Parameter

Select the potency type to be examined by the test. The following potency types are available:

  • Relative potency
  • Absolute potency

Please consult the help page of the test for additional information.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 required none

Context:

/Quantitative response assay/Analysis/Suitability tests/Assay suitability tests/choice/Test: Log potency range (L-value)/

/Quantitative response assay/Analysis/Suitability tests/Sample suitability tests/choice/Test: Log potency range (L-value)/

/Test system definition (Quantitative response assay)/Suitability tests/Assay suitability tests/choice/Test: Log potency range (L-value)/

/Test system definition (Quantitative response assay)/Suitability tests/Sample suitability tests/choice/Test: Log potency range (L-value)/

Parameter

Select the Parameter to be examined by this test.

Important: Test definitions are ignored without notification if the Parameter you select results in invalid test definitions (for example, if a test cannot be performed for the model you use).

Please consult the help page of the test for additional information.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 required none

Context:

/Quantitative response assay/Analysis/Suitability tests/Assay suitability tests/choice/Equivalence test: Parameter estimate/

/Quantitative response assay/Analysis/Suitability tests/Sample suitability tests/choice/Equivalence test: Parameter estimate/

/Test system definition (Quantitative response assay)/Suitability tests/Assay suitability tests/choice/Equivalence test: Parameter estimate/

/Test system definition (Quantitative response assay)/Suitability tests/Sample suitability tests/choice/Equivalence test: Parameter estimate/

/Quantitative response assay/Analysis/Suitability tests/Assay suitability tests/choice/Equivalence test: Difference of parameter estimates/

/Quantitative response assay/Analysis/Suitability tests/Sample suitability tests/choice/Equivalence test: Difference of parameter estimates/

/Test system definition (Quantitative response assay)/Suitability tests/Assay suitability tests/choice/Equivalence test: Difference of parameter estimates/

/Test system definition (Quantitative response assay)/Suitability tests/Sample suitability tests/choice/Equivalence test: Difference of parameter estimates/

/Quantitative response assay/Analysis/Suitability tests/Assay suitability tests/choice/Equivalence test: Ratio of parameter estimates/

/Quantitative response assay/Analysis/Suitability tests/Sample suitability tests/choice/Equivalence test: Ratio of parameter estimates/

/Test system definition (Quantitative response assay)/Suitability tests/Assay suitability tests/choice/Equivalence test: Ratio of parameter estimates/

/Test system definition (Quantitative response assay)/Suitability tests/Sample suitability tests/choice/Equivalence test: Ratio of parameter estimates/

/Quantitative response assay/Analysis/Suitability tests/Assay suitability tests/choice/Equivalence test: Scaled parameter range/

/Quantitative response assay/Analysis/Suitability tests/Sample suitability tests/choice/Equivalence test: Scaled parameter range/

/Test system definition (Quantitative response assay)/Suitability tests/Assay suitability tests/choice/Equivalence test: Scaled parameter range/

/Test system definition (Quantitative response assay)/Suitability tests/Sample suitability tests/choice/Equivalence test: Scaled parameter range/

/Quantitative response assay/Analysis/Suitability tests/Assay suitability tests/choice/Point estimate test: Parameter estimate/

/Quantitative response assay/Analysis/Suitability tests/Sample suitability tests/choice/Point estimate test: Parameter estimate/

/Test system definition (Quantitative response assay)/Suitability tests/Assay suitability tests/choice/Point estimate test: Parameter estimate/

/Test system definition (Quantitative response assay)/Suitability tests/Sample suitability tests/choice/Point estimate test: Parameter estimate/

/Quantitative response assay/Analysis/Suitability tests/Assay suitability tests/choice/Point estimate test: Difference of parameter estimates/

/Quantitative response assay/Analysis/Suitability tests/Sample suitability tests/choice/Point estimate test: Difference of parameter estimates/

/Test system definition (Quantitative response assay)/Suitability tests/Assay suitability tests/choice/Point estimate test: Difference of parameter estimates/

/Test system definition (Quantitative response assay)/Suitability tests/Sample suitability tests/choice/Point estimate test: Difference of parameter estimates/

/Quantitative response assay/Analysis/Suitability tests/Assay suitability tests/choice/Point estimate test: Ratio of parameter estimates/

/Quantitative response assay/Analysis/Suitability tests/Sample suitability tests/choice/Point estimate test: Ratio of parameter estimates/

/Test system definition (Quantitative response assay)/Suitability tests/Assay suitability tests/choice/Point estimate test: Ratio of parameter estimates/

/Test system definition (Quantitative response assay)/Suitability tests/Sample suitability tests/choice/Point estimate test: Ratio of parameter estimates/

/Quantitative response assay/Analysis/Suitability tests/Assay suitability tests/choice/Test: Normalized difference of asymptotes/

/Quantitative response assay/Analysis/Suitability tests/Sample suitability tests/choice/Test: Normalized difference of asymptotes/

/Test system definition (Quantitative response assay)/Suitability tests/Assay suitability tests/choice/Test: Normalized difference of asymptotes/

/Test system definition (Quantitative response assay)/Suitability tests/Sample suitability tests/choice/Test: Normalized difference of asymptotes/

Point estimate test: Difference of parameter estimates

Add one or several tests for the difference of the Test or Control sample parameter minus the Standard sample parameter to your assay. To add the tests as assay suitability tests, add them as children of the Assay suitability tests element. To add the tests as sample suitability tests, add them as children of the Sample suitability tests element.

Important: Test definitions are ignored without notification if the Parameter you select results in invalid test definitions (for example, if a test cannot be performed for the model you use).

To pass the test, the difference between the Standard sample parameter and the Test or Control sample parameter has to be greater than or equal to the Lower margin and less than or equal to the Upper margin.

The following table lists all available tests and indicates which models and assay elements they support:

Point estimate test on the difference of the: Linear parallel-line model 4-parameter logistic model 5-parameter logistic model 3-parameter logistic model with fixed lower or upper asymptote Slope ratio model Assay elements
Upper asymptotes (A) (nonlinear models) no yes yes with fixed Lower asymptote no Test, Control
B parameters (nonlinear models) no yes yes yes no Test, Control
C parameters (nonlinear models) no yes yes yes no Test, Control
Lower asymptotes (D) (nonlinear models) no yes yes with fixed Upper asymptote no Test, Control
Asymmetry parameters (G) (nonlinear models) no no yes no no Test, Control
Slopes (nonlinear models) no yes yes yes no Test, Control
Intercepts (linear models) yes no no no yes Test, Control
Slopes (linear models) yes no no no yes Test, Control
Differences of asymptotes (A – D) (nonlinear models) no yes yes yes no Test, Control

Scope of the test

Important: Test definitions are ignored without notification if the scope you select results in invalid test definitions (for example, if a test cannot be performed for the assay element type you select).

The following table indicates how the scope of the test affects inclusion of various assay elements in tests:

Scope of the test Calculations by the test
All assay elements Runs the test for every assay element except Standard sample and Control lines.
Test samples only Runs the test for every Test sample.
Control samples only Runs the test for every Control sample.

This element has the following attributes:

Data type Multiplicity Usage Default value
Node 0...unbounded optional none

Context:

/Quantitative response assay/Analysis/Suitability tests/Assay suitability tests/choice/

/Quantitative response assay/Analysis/Suitability tests/Sample suitability tests/choice/

/Test system definition (Quantitative response assay)/Suitability tests/Assay suitability tests/choice/

/Test system definition (Quantitative response assay)/Suitability tests/Sample suitability tests/choice/

Point estimate test: Parameter estimate

Add one or several tests for single parameters to your assay. To add the tests as assay suitability tests, add them as children of the Assay suitability tests element. To add the tests as sample suitability tests, add them as children of the Sample suitability tests element.

Important: Test definitions are ignored without notification if the Parameter you select results in invalid test definitions (for example, if a test cannot be performed for the model you use).

To pass the test, the Parameter has to be between the Lower and Upper margin.

The following table lists all available tests and indicates which models and assay elements they support:

Point estimate test on the: Linear parallel-line model 4-parameter logistic model 5-parameter logistic model 3-parameter logistic model with fixed lower or upper asymptote Slope ratio model Assay elements
Upper asymptote (A) (nonlinear models) no yes yes with fixed Lower asymptote no Standard, Test, Control
B parameter (nonlinear models) no yes yes yes yes Standard, Test, Control
C parameter (nonlinear models) no yes yes yes no Standard, Test, Control
Lower asymptote (D) (nonlinear models) no yes yes with fixed Upper asymptote no Standard, Test, Control
Asymmetry parameter (G) (nonlinear models) no no yes no no Standard, Test, Control
Intercept (linear models) yes no no no yes Standard, Test, Control
Slope (linear models) yes no no no yes Standard, Test, Control
Slope (nonlinear models) no yes yes with fixed Upper asymptote no Standard, Test, Control
Difference of asymptotes (A - D) (nonlinear models) no yes yes no no Standard, Test, Control
Ratio of asymptotes (A / D) (nonlinear models) no yes yes no no Standard, Test, Control
Pure error (mean squares) yes yes yes yes yes Standard, Test, Control
Residual error (mean squares) yes yes yes yes yes Standard, Test, Control

Scope of the test

Important: Test definitions are ignored without notification if the scope you select results in invalid test definitions (for example, if a test cannot be performed for the assay element type you select).

The following table indicates how the scope of the test affects inclusion of various assay elements in tests:

Scope of the test Calculations by the test
All assay elements Runs the test for every assay element except Control lines.
Standard only Runs the test for the Standard sample.
Test samples only Runs the test for every Test sample.
Control samples only Runs the test for every Control sample.

This element has the following attributes:

Data type Multiplicity Usage Default value
Node 0...unbounded optional none

Context:

/Quantitative response assay/Analysis/Suitability tests/Assay suitability tests/choice/

/Quantitative response assay/Analysis/Suitability tests/Sample suitability tests/choice/

/Test system definition (Quantitative response assay)/Suitability tests/Assay suitability tests/choice/

/Test system definition (Quantitative response assay)/Suitability tests/Sample suitability tests/choice/

Point estimate test: Ratio of parameter estimates

Add one or several tests for the ratio of the Test or Control sample parameter over the Standard sample parameter to your assay. To add the tests as assay suitability tests, add them as children of the Assay suitability tests element. To add the tests as sample suitability tests, add them as children of the Sample suitability tests element.

Important: Test definitions are ignored without notification if the Parameter you select results in invalid test definitions (for example, if a test cannot be performed for the model you use).

To pass the test, the ratio of the Test or Control sample parameter to the Standard sample parameter has to be greater than the Lower margin and less than the Upper margin.

The following table lists all available tests and indicates which models and assay elements they support:

Point estimate test on the ratio of the: Linear parallel-line model 4-parameter logistic model 5-parameter logistic model 3-parameter logistic model with fixed lower or upper asymptote Slope ratio model Assay elements
Upper asymptotes (A) (nonlinear models) no yes yes with fixed Lower asymptote no Test, Control
B parameters (nonlinear models) no yes yes yes no Test, Control
C parameters (nonlinear models) no yes yes yes no Test, Control
Lower asymptotes (D) (nonlinear models) no yes yes with fixed Upper asymptote no Test, Control
Asymmetry parameters (G) (nonlinear models) no no yes no no Test, Control
Slopes (nonlinear models) no yes yes yes no Test, Control
Intercepts (linear models) yes no no no yes Test, Control
Slopes (linear models) yes no no no yes Test, Control
Differences of asymptotes (A - D) (nonlinear models) no yes yes yes no Test, Control

Scope of the test

Important: Test definitions are ignored without notification if the scope you select results in invalid test definitions (for example, if a test cannot be performed for the assay element type you select).

The following table indicates how the scope of the test affects inclusion of various assay elements in tests:

Scope of the test Calculations by the test
All assay elements Runs the test for every assay element except Standard sample and Control lines.
Test samples only Runs the test for every Test sample.
Control samples only Runs the test for every Control sample.

This element has the following attributes:

Data type Multiplicity Usage Default value
Node 0...unbounded optional none

Context:

/Quantitative response assay/Analysis/Suitability tests/Assay suitability tests/choice/

/Quantitative response assay/Analysis/Suitability tests/Sample suitability tests/choice/

/Test system definition (Quantitative response assay)/Suitability tests/Assay suitability tests/choice/

/Test system definition (Quantitative response assay)/Suitability tests/Sample suitability tests/choice/

Point estimate tests: Difference of parameter estimates

Select the tests for which you want to develop margins. In this section, you can select tests for the difference of the Test or Control sample parameter minus the Standard sample parameter.

This element has the following attributes:

Data type Multiplicity Usage Default value
Node 0...1 optional none

Context:

/Equivalence margin development (Quantitative response assays)/Margin development/

Point estimate tests: Difference of parameter estimates

Select the tests you want to use to define your test strategy. In this section, you can select tests for the difference of the Test or Control sample parameter minus the Standard sample parameter.

This element has the following attributes:

Data type Multiplicity Usage Default value
Node 0...1 optional none

Context:

/Equivalence margin development (Quantitative response assays)/Test strategies/Strategy/

Point estimate tests: Parameter estimate

Select the tests for which you want to develop margins. In this section, you can select tests for single parameters.

This element has the following attributes:

Data type Multiplicity Usage Default value
Node 0...1 optional none

Context:

/Equivalence margin development (Quantitative response assays)/Margin development/

Point estimate tests: Parameter estimate

Select the tests you want to use to define your test strategy. In this section, you can select tests for single parameters.

This element has the following attributes:

Data type Multiplicity Usage Default value
Node 0...1 optional none

Context:

/Equivalence margin development (Quantitative response assays)/Test strategies/Strategy/

Point estimate tests: Ratio of parameter estimates

Select the tests for which you want to develop margins. In this section, you can select tests for the ratio of the Test or Control sample parameter over the Standard sample parameter.

This element has the following attributes:

Data type Multiplicity Usage Default value
Node 0...1 optional none

Context:

/Equivalence margin development (Quantitative response assays)/Margin development/

Point estimate tests: Ratio of parameter estimates

Select the tests you want to use to define your test strategy. In this section, you can select tests for the ratio of the Test or Control sample parameter over the Standard sample parameter.

This element has the following attributes:

Data type Multiplicity Usage Default value
Node 0...1 optional none

Context:

/Equivalence margin development (Quantitative response assays)/Test strategies/Strategy/

Potency confidence interval calculation method

Defines how the potency confidence interval is calculated. The following options are available from the drop-down list:

  • Based on ANOVA error: Adjusts potency confidence intervals by (1) the pure error for Pure-error ANOVA and (2) the residual error (of the full model) for Residual-error ANOVA.
  • Based on error of restricted model: Adjusts potency confidence intervals by the residual error of the restricted fit.
Note: With linear parallel-line assays, the error based on the ANOVA model is commonly used, and this is the default in previous PLA versions. With nonlinear models, the restricted-model error is more common. Yet, if the Residual-error ANOVA option is selected, previous PLA versions also use the restricted-model error to evaluate linear models. Otherwise, they use the error based on the ANOVA model.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 required none

Context:

/Quantitative response assay/Analysis/Analytical model/Advanced settings/

Potency data

This section allows you to adjust the dataset structure used to summarize reportable values generated by Combination of assay results documents.

Note: Much of the data table is populated from assay documents. These data may not be visible in the Content editor.

Expand the node to add or view information.

This element has the following attributes:

Data type Multiplicity Usage Default value
Node 1...1 required none

Context:

/Combination of independent assay results/Setup/

Potency estimation confidence level

Select the confidence level of the potency confidence interval. A common value is 95%.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:double 1...1 required none

Context:

/Quantitative response assay/Analysis/Analytical model/

Potency type

Select a Potency type from the drop-down list: Relative potency, Raw material potency, or Stock solution potency. The test uses the Potency type you select.

Note: The Potency type you select for the test needs to match the potencies defined in the Preparation schemes. If the assay does not calculate potencies of the selected type, the test returns an 'NC' (not calculated).

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 0...1 optional none

Context:

/Quantitative response assay/Analysis/Suitability tests/Assay suitability tests/choice/Test: Potency value/

/Quantitative response assay/Analysis/Suitability tests/Assay suitability tests/choice/Test: Potency confidence interval/

/Quantitative response assay/Analysis/Suitability tests/Sample suitability tests/choice/Test: Potency value/

/Quantitative response assay/Analysis/Suitability tests/Sample suitability tests/choice/Test: Potency confidence interval/

/Test system definition (Quantitative response assay)/Suitability tests/Assay suitability tests/choice/Test: Potency value/

/Test system definition (Quantitative response assay)/Suitability tests/Assay suitability tests/choice/Test: Potency confidence interval/

/Test system definition (Quantitative response assay)/Suitability tests/Sample suitability tests/choice/Test: Potency value/

/Test system definition (Quantitative response assay)/Suitability tests/Sample suitability tests/choice/Test: Potency confidence interval/

Potency type

Select a Potency type from the drop-down list: Absolute potency, Relative potency, or Relative and absolute potency.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 required none

Context:

/Combination of independent assay results/Analysis/

Predilution factor

Enter a single predilution factor. The calculation uses the reciprocal value (1 / Predilution factor).

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:double 0...unbounded optional none

/Basic bioassay protocol/choice/Mode: Assay element/Standard sample/choice/Predilution factors: Manual input/

/Basic bioassay protocol/choice/Mode: Assay element/Test sample/choice/Predilution factors: Manual input/

/Basic bioassay protocol/choice/Mode: Assay element/Control sample/choice/Predilution factors: Manual input/

/Quantitative response assay/Setup/Preparation schemes/Preparation scheme/Predilution factors/

Predilution factors

Select this option if you want to provide predilution factors directly. To add a Predilution factor: Double-click Predilution factor in the Creatable elements pane. When the assays are analyzed, a final predilution factor is calculated by multiplying all predilution factors entered here.

Note: Predilution factors are considered after relative potency is calculated. They do not enter the calculation for model fit.

This element has the following attributes:

Data type Multiplicity Usage Default value
Node 1...1 required none

Context:

/Quantitative response assay/Setup/Preparation schemes/Preparation scheme/

Predilution factors: Defined by template

Select this option if you want to use the assay template settings to define the predilution factors.

If you do not use this option, the settings provided in the Basic bioassay protocol are used for the predilution factors in the generated assay replicates.

This element has the following attributes:

Data type Multiplicity Usage Default value
Empty 1...1 required none

Context:

/Basic bioassay protocol/choice/Mode: Assay element/Standard sample/choice/

/Basic bioassay protocol/choice/Mode: Assay element/Test sample/choice/

/Basic bioassay protocol/choice/Mode: Assay element/Control sample/choice/

Predilution factors: Manual input

Select this option if you want to provide predilution factors directly. To add a Predilution factor: Double-click Predilution factor in the Creatable elements pane.

When the assays are analyzed, a final predilution factor is calculated by multiplying all predilution factors entered here.

Note: Predilution factors are considered after relative potency is calculated. They do not enter the calculation for model fit.

This element has the following attributes:

Data type Multiplicity Usage Default value
Node 1...1 required none

Context:

/Basic bioassay protocol/choice/Mode: Assay element/Standard sample/choice/

/Basic bioassay protocol/choice/Mode: Assay element/Test sample/choice/

/Basic bioassay protocol/choice/Mode: Assay element/Control sample/choice/

Preparation scheme

Assign a Preparation scheme to this assay element. Preparation schemes define dilution sequences, absolute potencies, and predilution settings of assay elements.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:string 1...1 required none

Context:

/Quantitative response assay/Setup/Assay elements/Standard sample/

/Quantitative response assay/Setup/Assay elements/Test sample/

/Quantitative response assay/Setup/Assay elements/Control sample/

/Quantitative response assay/Setup/Assay elements/Control line/

Preparation scheme

This section allows you to define a Preparation scheme. Preparation schemes contain settings on dose sequence, absolute potency, and predilution factors. In every assay element, you must reference exactly one Preparation scheme.

Tip: You can reference any Preparation scheme from more than one assay element.

Expand the node to add or view information.

This element has the following attributes:

Data type Multiplicity Usage Default value
Node 1...unbounded required none

Context:

/Quantitative response assay/Setup/Preparation schemes/

Preparation schemes

This section allows you to set up multiple preparation schemes to define doses and dimensions of your treatments. All assay elements are associated with the first preparation scheme by default. Add additional preparation schemes as you require.

Tip: Use the context menu or Creatable elements pane to add Preparation schemes.

Expand the node to add or view information.

This element has the following attributes:

Data type Multiplicity Usage Default value
Node 1...1 required none

Context:

/Quantitative response assay/Setup/

Property filter

Define a section property filter to be used for data aggregation.

This element has the following attributes:

Data type Multiplicity Usage Default value
Node 0...1 required none

Context:

Data type Multiplicity Usage Default value
Node 1...unbounded required none

Context:

Data type Multiplicity Usage Default value
Node 0...unbounded optional none

/Equivalence margin development (Quantitative response assays)/Data table/Column: Assay element/

/Quantitative response assay/Setup/Observation data/Column: Section/

Property key

Select a Property key to identify the data to be aggregated.

Note: The key only applies to document aggregation.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 required none

/Basic bioassay protocol/Reportable values/Document reference/Document property filter/

/Combination of independent assay results/Setup/Potency data/Column: Document reference/Document property filter/

/Equivalence margin development (Quantitative response assays)/Data table/Column: Document reference/Document property filter/

/Quantitative response assay/Setup/Observation data/Column: Document reference/Document property filter/

Property key

Select the key of the document property you want to use. Only documents in which an element has this property key will be considered for the import.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 required none

/Basic bioassay protocol/Templates/Combination calculation templates/Configuration/Template/Config/Document property filter/

/Basic bioassay protocol/Comment/Linked document/Config/Document property filter/

/Combination of independent assay results/Comment/Linked document/Config/Document property filter/

/Equivalence margin development (Quantitative response assays)/Comment/Linked Document/Config/Document property filter/

/Quantitative response assay/Comment/Linked document/Config/Document property filter/

/Test system definition (Quantitative response assay)/Comment/Linked document/Config/Document property filter/

Property key

Select the key of the document property you want to use. The key specifies which data element of the linked document is to be imported into this document.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 required none

/Basic bioassay protocol/Comment/Linked document/Config/Document property import/

/Combination of independent assay results/Comment/Linked document/Config/Document property import/

/Equivalence margin development (Quantitative response assays)/Comment/Linked Document/Config/Document property import/

/Quantitative response assay/Comment/Linked document/Config/Document property import/

/Test system definition (Quantitative response assay)/Comment/Linked document/Config/Document property import/

Property key

Currently, no information available.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 required none

Context:

/Equivalence margin development (Quantitative response assays)/Data table/Column: Assay element/Property filter/

Property key

Select the key of the section property you want to use. Only documents in which an element has this property key will be considered for the import.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 required none

/Basic bioassay protocol/Templates/Combination calculation templates/Configuration/Template/Config/Section property filter/

/Basic bioassay protocol/Comment/Linked document/Config/Section property filter/

/Combination of independent assay results/Comment/Linked document/Config/Section property filter/

/Equivalence margin development (Quantitative response assays)/Comment/Linked Document/Config/Section property filter/

/Quantitative response assay/Comment/Linked document/Config/Section property filter/

/Test system definition (Quantitative response assay)/Comment/Linked document/Config/Section property filter/

Property key

Select the key of the section property you want to use. The key specifies which data element of the linked document is to be imported into this document.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 1...1 required none

/Basic bioassay protocol/Comment/Linked document/Config/Section property import/

/Combination of independent assay results/Comment/Linked document/Config/Section property import/

/Equivalence margin development (Quantitative response assays)/Comment/Linked Document/Config/Section property import/

/Quantitative response assay/Comment/Linked document/Config/Section property import/

/Test system definition (Quantitative response assay)/Comment/Linked document/Config/Section property import/

Property scope

Select a Property scope from the drop-down list.

Note: The scope only applies to document aggregation.

The following options are available to specify the source of the aggregated property:

  • Document
  • Section

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 0...1 optional none

/Combination of independent assay results/Setup/Potency data/Column: Exclude from analysis/

/Equivalence margin development (Quantitative response assays)/Data table/Column: Exclude assay/

/Quantitative response assay/Setup/Observation data/Column: Observation group/

Protect observation group ID

Select how you want to protect observation group IDs in the Quantitative response assays you generate.

The following options are available:

  • 'Always': In the Quantitative response assay documents you generate, observation group IDs are always protected.
  • 'Defined by template': In the Quantitative response assay documents you generate, observation group IDs are only protected if this is defined in the templates you use to generate the documents.

This element has the following attributes:

Data type Multiplicity Usage Default value
xs:token 0...1 optional none

Context:

/Basic bioassay protocol/Templates/Assay templates/