These classes and methods facilitate navigation of the Affymetrix ARR sample attribute files. ARR files are generated by the Affymetrix AGCC (GeneChip(R) Command Console) application. Specifically, the classes are R representations of the Affymetrix classes defined in ArraySetAndTemplateFile.dtd. The 'show' methods for these classs indicate how objects are to be accessed; details are in the ‘Retrieving MAGE and ARR sample attributes’ vignette.
Objects are created internally, by parsing XML retrieved from ARR, and are not created directly by the user.
Objects have a variety of slots. To discover slot names and content
type, see the
slotNames portion of the example, below.
"AffyCompatible", by class "ARRCompatibility", distance 2.
'Accessor' methods are defined on auto-generated classes to access slot content.
Accessors are apparent from displaying the object; each line of the
display is of the form
accessor: content. To retrieve the
content of an instance
Some objects contains several instances of another object. These
'typed associations' are represented by the
.TypedAssociation class, and are navigated or
subset as one would a standard R vector, e.g., using
[[. A useful paradigm for displaying all instances is
illustrated in the vignette.
Martin Morgan <[email protected]>
Vignette ‘Retrieving MAGE and ARR sample attributes’.
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