Analysis Options

Data Aggregation Method

The value selected for the Data Aggregation Method option determines how aggregate signal levels and consensus data views will be calculated, using means or medians.

  • Individal - When Individual is selected for the Replicate Data option, each individual Observation Block item will be subjected to the requested analytical procedures and will appear in the resulting analytical output as a result item.
  • Consensus - When Consensus is selected for the Replicate Data option, replicate Observation Block items will be merged into a single consensus Observation Block representation, and the consensus Observation Block item will be subjected to the requested analytical procedures and will appear in the resulting analytical output as a result item.

Replicate Data

The value selected for the Replicate Data option determines how replicate Observation Block items will be handled.

  • Individual- When Individual is selected for the Replicate Data option, each individual Observation Block item will be subjected to the requested analytical procedures and will appear in the resulting analytical output as a result item.
  • Consensus - When Consensus is selected for the Replicate Data option, replicate Observation Block items will be merged into a single consensus Observation Block representation, and the consensus Observation Block item will be subjected to the requested analytical procedures and will appear in the resulting analytical output as a result item.

Resample Method

The selected algorithm is used to define the consensus sampling for the Observation Block that will be the merged representation Observation Block replicate items.

  • Basic - The Basic Resampling algorithm provides a consensus sampling that represents each distinct concentration value in any of the individual replicate items for each test substance. Distinct concentration values are rounded to the nearest value within the precision specified for the option Resample Precision.
  • Regular - The Regular Resampling algorithm provides a consensus sampling that is the fixed dilution factor which is the best match for the concentrations represented by the individual replicate items for each test substance. The minimum acceptable sampling is controlled by the Minimum Sample parameter of the algorithm.

Consensus Aggregation Ext

  • When the Replicate Data option has the value Consensus, the value of Consensus Aggregation Ext defines additional protocol parameters that will be used to determine replicate Observation Block items. The value of Consensus Aggregation Ext is a semicolon delimited list of parameter names defined by the Datasource and Protocol.

Dose Response Characterization

  • Logistic Curve - Dose response data will undergo curve-fitting using a 3 or 4 parameter curve (see Logistic Curve Parameters below).
  • Linear Interpolation - Dose response data is fit exactly to the data.

Logistic Curve Parameters

If using Logistic Curve for Dose Response Characterization, choose the best fit for your data here.

  • 3 Parameter - Allows you to fix the base value (min).
  • 4 Parameter - Base value is taken from data.

Extract Dose Series from Dose Matrix

If single-agent data was not collected, Chalice will attempt to extract single-agent attributes (like dose-response curves) from the combination dose-matrices.

Combination Interpretation

Certain models, such as HSA, tend to overestimate and can be tempered using the pessimistic option here. By contrast, the Loewe model is naturally more pessimistic (realistic).

Test Substance Orientation

Test substances and/or substance mixtures are oriented canonically in multi dimensional Observation Block items to ensure consistent presentation.

  • Default - Default canonical orientation is used to produce analytical output.
  • Reversed - Reverse canonical orientation is used to produce analytical output.

Analytical Output

The value selected for the Analytical Output option determines the scope of analytical procedures to which the Obervation Block items are subjected.

  • Minimal - The minimal analytical output is created for each Observation Block item.
  • Full - The full analytical output is created for each Observation Block item.

Selected Measure

Select the appropriate measure for your data or use 'Automatic' if you are unsure.

Isobolograph Level

 

Analytical Aggregation

 

Self Cross Matrix Interpretation

 

Response Area Range

Limit the response area minimum and maximum.

Limit Concentration Range

Limit the the output to a specified concentration range (unit default = uM, compound names are case-insensitive).

Desired effect Example
Limit all compounds in uM * [0 to 5]
Limit multiple compounds with wildcard in nM amox* [10nM to 50nM]; bufex* [25nM to 100nM]
Limit specific compounds in pM amoxopine [200pM to 850pM]

Masking

Use this feature to speed up processing time for large data sets. Downsampling dose matrices can save many computational cycles, often without diminishing the ability to gather meaningful insights from the result set.