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


Package Samples:

org.biomage.BioAssay
org.biomage.BioAssayData

Classes:

BioAssay_package: Provides classes that contain information and annotation on the event of joining an Array with a BioMaterial preparation, the acquisition of images and the extraction of data on a per feature basis from those images. The derived classes of BioAssay represent the base PhysicalBioAssays which lead to the production of Images, the MeasuredBioAssay which is associated with the set of quantitations produced by FeatureExtraction, and DerivedBioAssay (see BioAssayData package) which groups together BioAssays that have been analyzed together to produce further refinement of the quantitations. The design ...
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.
MeasuredBioAssay: A measured bioAssay is the direct processing of information in a physical bioAssay by the featureExtraction event. Often uses images which are referenced through the physical bioAssay.
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.
PhysicalBioAssay: A bioAssay created by the bioAssayCreation event (e.g. in gene expression analysis this event is represented by the hybridization event).
QuantitationTypeMap: A QuantitationTypeMap is the description of how source QuantitationTypes are mathematically transformed into a target QuantitationType.
Image: An image is created by an imageAcquisition event, typically by scanning the hybridized array (the PhysicalBioAssay).
BioAssayTreatment: The event which records the process by which PhysicalBioAssays are processed (typically washing, blocking, etc...).
DerivedBioAssay: A BioAssay that is created by the Transformation BioEvent from one or more MeasuredBioAssays or DerivedBioAssays.
DesignElementMap: A DesignElementMap is the description of how source DesignElements are transformed into a target DesignElement.

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