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org.biomage.BioAssayData: Javadoc index of package org.biomage.BioAssayData.


Package Samples:

org.biomage.BioAssayData

Classes:

BioAssayData_package: The classes defined here provide data and the information and annotation on the derivation of that data. Some of the scenarios that might occur are the following. FeatureExtraction of a single PhysicalBioAssay produces MeasuredBioAssayData that has a single BioAssay on the BioAssayDimension, typically the Features described in the ArrayDesign on the DesignElementDimension, and the Quantitations associated with the application of a FeatureExtraction protocol on the QuantitationDimension. An error model transformation might be applied that doesn't change the BioAssayDimension or the DesignElementDimension ...
BioAssayData: Represents the dataset created when the BioAssays are created. BioAssayData is the entry point to the values. Because the actual values are represented by a different object, BioDataValues, which can be memory intensive, the annotation of the transformation can be gotten separate from the data.
Transformation: The process by which derivedBioAssays are created from measuredBioAssays and/or derivedBioAssays. It uses mappings to indicate the input and output dimensions.
BioAssayMap: The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays.
QuantitationTypeMap: A QuantitationTypeMap is the description of how source QuantitationTypes are mathematically transformed into a target QuantitationType.
DesignElementMap: A DesignElementMap is the description of how source DesignElements are transformed into a target DesignElement.
QuantitationTypeMapping: Container of the mappings of the input QuantitationType dimensions to the output QuantitationType dimension.
DesignElementMapping: Container of the mappings of the input DesignElement dimensions to the output DesignElement dimension.
BioAssayMapping: Container of the mappings of the input BioAssay dimensions to the output BioAssay dimension.
DesignElementDimension: An ordered list of designElements. It will be realized as one of its three subclasses.
MeasuredBioAssayData: The data associated with the MeasuredBioAssay produced by FeatureExtraction.
BioAssayDatum: A single cell of the quantitation, bioAssay, designElement matrix.
CompositeSequenceDimension: Specialized DesignElementDimension to hold CompositeSequences.

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