MultiSet               package:Biobase               R Documentation

Class to Contain and Describe High-Throughput Expression Level Assays.

Description:

     Container for high-throughput assays and experimental metadata.
     'MutliSet' is derived from 'eSet-class'. 'MultiSet' differs from
     'ExpressionSet-class' because 'MultiSet' can contain any
     element(s) in 'assayData' ('ExpressionSet' must have an element
     named 'exprs').

Extends:

     Directly extends class 'eSet'.

Creating Objects:

     'new('MultiSet', phenoData = [AnnotatedDataFrame], experimentData
     = [MIAME], annotation = [character], protocolData =
     [AnnotatedDataFrame], ...) '

     'updateOldESet(oldESet,"MultiSet")'

     'MultiSet' instances are usually created through 'new("MultiSet",
     ...)'. The '...' arguments to 'new' are matrices of expression
     data (with features corresponding to rows and samples to columns),
     'phenoData', 'experimentData', 'annotation', and 'protocolData'. 
     'phenoData', 'experimentData', 'annotation', and 'protocolData'
     can be missing, in which case they are assigned default values.

     'updateOldESet' will take a serialized instance (e.g., saved to a
     disk file with 'save' object created with earlier definitions of
     the 'eSet-class', and update the object to 'MultiSet'. Warnings
     are issued when direct translation is not possible; incorrectly
     created 'oldESet' instances may not be updated.

Slots:

     Inherited from 'eSet':

     'assayData': Contains zero or more matrices with equal dimensions,
          and with column number equal to 'nrow(phenoData)'. Each
          matrix in 'assayData' has rows representing features (e.g.,
          reporters) and columns representing samples.
          Class:'AssayData-class'

     'phenoData': See 'eSet-class'

     'experimentData': See 'eSet-class'

     'annotation': See 'eSet-class'

     'protocolData': See 'eSet-class'

Methods:

     Class-specific methods: none

     Derived from 'eSet-class':

     'updateObject(object, ..., verbose=FALSE)' Update instance to
          current version, if necessary. See 'updateObject' and 'eSet'

     'isCurrent(object)' Determine whether version of object is
          current. See 'isCurrent'

     'isVersioned(object)' Determine whether object contains a
          'version' string describing its structure . See 'isVersioned'

     'sampleNames(MultiSet)' and 'sampleNames(MultiSet)<-': See
          'eSet-class'

     'featureNames(MultiSet)', 'featureNames(MultiSet, value)<-': See
          'eSet-class'

     'dims(MultiSet)': See 'eSet-class'

     'phenoData(MultiSet)', 'phenoData(MultiSet,value)<-': See
          'eSet-class'

     'varLabels(MultiSet)', 'varLabels(MultiSet, value)<-': See
          'eSet-class'

     'varMetadata(MultiSet)', 'varMetadata(MultiSet,value)<-': See
          'eSet-class'

     'pData(MultiSet)', 'pData(MultiSet,value)<-': See 'eSet-class'

     'varMetadata(MultiSet)', 'varMetadata(MultiSet,value)' See
          'eSet-class'

     'experimentData(MultiSet)','experimentData(MultiSet,value)<-': See
          'eSet-class'

     'pubMedIds(MultiSet)', 'pubMedIds(MultiSet,value)' See
          'eSet-class'

     'abstract(MultiSet)': See 'eSet-class'

     'annotation(MultiSet)', 'annotation(MultiSet,value)<-' See
          'eSet-class'

     'protocolData(MultiSet)', 'protocolData(MultiSet,value)<-' See
          'eSet-class'

     'combine(MultiSet,MultiSet)': See 'eSet-class'

     'storageMode(eSet)', 'storageMode(eSet,character)<-': See
          'eSet-class'

     Standard generic methods:

     'initialize(MultiSet)': Object instantiation, used by 'new'; not
          to be called directly by the user.

     'validObject(MultiSet)': Validity-checking method, ensuring that
          all elements of 'assayData' are matricies with equal
          dimensions.

     'as(eSet,MultiSet)': Coerce the 'eSet' portion of an object to
          'MultiSet'.

     'show(MultiSet)' See 'eSet-class'

     'dim(MultiSet)', 'ncol' See 'eSet-class'

     'MultiSet[(index)': See 'eSet-class'

     'MultiSet$', 'MultiSet$<-' See 'eSet-class'

Author(s):

     Biocore team

See Also:

     'eSet-class', 'ExpressionSet-class'

Examples:

     # create an instance of ExpressionSet
     new("MultiSet")

