ExpressionSet            package:Biobase            R Documentation

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

Description:

     Container for high-throughput assays and experimental metadata.
     'ExpressionSet' class is derived from 'eSet', and requires a
     matrix named 'exprs' as assayData member.

Extends:

     Directly extends class 'eSet'.

Creating Objects:

     'new("ExpressionSet")'

     'new("ExpressionSet", phenoData = new("AnnotatedDataFrame"),
     featureData = new("AnnotatedDataFrame"), experimentData =
     new("MIAME"), annotation = character(0), protocolData =
     phenoData[,integer(0)], exprs = new("matrix")) '

     This creates an 'ExpressionSet' with 'assayData' implicitly
     created to contain 'exprs'. Additional named matrix arguments with
     the same dimensions as 'exprs' are added to 'assayData'; the row
     and column names of these additional matricies should match those
     of 'exprs'. 

     'new("ExpressionSet", assayData =
     assayDataNew(exprs=new("matrix")), phenoData =
     new("AnnotatedDataFrame"), featureData =
     new("AnnotatedDataFrame"), experimentData = new("MIAME"),
     annotation = character(0), protocolData = phenoData[,integer(0)])
     '

     This creates an 'ExpressionSet' with 'assayData' provided
     explicitly. In this form, the only required named argument is
     'assayData'.

     'as([exprSet],"ExpressionSet")'

     'ExpressionSet' instances are usually created through
     'new("ExpressionSet", ...)'. Usually the arguments to 'new'
     include 'exprs' (a matrix of expression data, with features
     corresponding to rows and samples to columns), 'phenoData',
     'featureData', 'experimentData', 'annotation', and 'protocolData'.
      'phenoData', 'featureData', 'experimentData', 'annotation', and
     'protocolData' can be missing, in which case they are assigned
     default values.

Slots:

     Inherited from 'eSet':

     'assayData': Contains matrices with equal dimensions, and with
          column number equal to 'nrow(phenoData)'. 'assayData' must
          contain a matrix 'exprs' with rows represening features
          (e.g., reporters) and columns representing samples.
          Additional matrices of identical size (e.g., representing
          measurement errors) may also be included in 'assayData'.
          Class:'AssayData-class'

     'phenoData': See 'eSet'

     'featureData': See 'eSet'

     'experimentData': See 'eSet'

     'annotation': See 'eSet'

     'protocolData': See 'eSet'

Methods:

     Class-specific methods.

     'as(exprSet,"ExpressionSet")' Coerce objects of 'exprSet-class' to
          'ExpressionSet'

     'as(object,"data.frame")' Coerce objects of 'ExpressionSet-class'
          to 'data.frame' by transposing the expression matrix and
          concatenating 'phenoData'

     'exprs(ExpressionSet)', 'exprs(ExpressionSet,matrix)<-' Access and
          set elements named 'exprs' in the 'AssayData-class' slot.

     'esApply(ExpressionSet, MARGIN, FUN,          ...)' 'apply'-like
          function to conveniently operate on 'ExpressionSet' objects.
          See 'esApply'.

     'write.exprs(ExpressionSet)' Write expression values to a text
          file. It takes the same arguments as 'write.table'

     Derived from 'eSet':

     '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'

     'assayData(ExpressionSet)': See 'eSet'

     'sampleNames(ExpressionSet)' and 'sampleNames(ExpressionSet)<-': 
          See 'eSet'

     'featureNames(ExpressionSet)', 'featureNames(ExpressionSet, value)<-': 
          See 'eSet'

     'dims(ExpressionSet)': See 'eSet'

     'phenoData(ExpressionSet)', 'phenoData(ExpressionSet,value)<-': 
          See 'eSet'

     'varLabels(ExpressionSet)', 'varLabels(ExpressionSet, value)<-': 
          See 'eSet'

     'varMetadata(ExpressionSet)', 'varMetadata(ExpressionSet,value)<-': 
          See 'eSet'

     'pData(ExpressionSet)', 'pData(ExpressionSet,value)<-': See 'eSet'

     'varMetadata(ExpressionSet)', 'varMetadata(ExpressionSet,value)' 
          See 'eSet'

     'experimentData(ExpressionSet)','experimentData(ExpressionSet,value)<-': 
          See 'eSet'

     'pubMedIds(ExpressionSet)', 'pubMedIds(ExpressionSet,value)' See
          'eSet'

     'abstract(ExpressionSet)': See 'eSet'

     'annotation(ExpressionSet)', 'annotation(ExpressionSet,value)<-' 
          See 'eSet'

     'protocolData(ExpressionSet)', 'protocolData(ExpressionSet,value)<-' 
          See 'eSet'

     'combine(ExpressionSet,ExpressionSet)': See 'eSet'

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

     Standard generic methods:

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

     'updateObject(ExpressionSet)': Update outdated versions of
          'ExpressionSet' to their current definition. See
          'updateObject', 'Versions-class'.

     'validObject(ExpressionSet)': Validity-checking method, ensuring
          that 'exprs' is a member of 'assayData'.
          'checkValidity(ExpressionSet)' imposes this validity check,
          and the validity checks of 'eSet'.

     'makeDataPackage(object, author, email, packageName, packageVersion, license, biocViews, filePath, description=paste(abstract(object), collapse="nn"), ...)' 
          Create a data package based on an ExpressionSet object. See
          'makeDataPackage'.

     'as(exprSet,ExpressionSet)': Coerce 'exprSet' to 'ExpressionSet'.

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

     'show(ExpressionSet)' See 'eSet'

     'dim(ExpressionSet)', 'ncol' See 'eSet'

     'ExpressionSet[(index)': See 'eSet'

     'ExpressionSet$', 'ExpressionSet$<-' See 'eSet'

     'ExpressionSet[[i]]', 'ExpressionSet[[i]]<-' See 'eSet'

Author(s):

     Biocore team

See Also:

     'eSet-class', 'ExpressionSet-class'.

Examples:

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

     new("ExpressionSet",
         exprs=matrix(runif(1000), nrow=100, ncol=10))

     # update an existing ExpressionSet
     data(sample.ExpressionSet)
     updateObject(sample.ExpressionSet)

     # information about assay and sample data
     featureNames(sample.ExpressionSet)[1:10]
     sampleNames(sample.ExpressionSet)[1:5]
     phenoData(sample.ExpressionSet)
     experimentData(sample.ExpressionSet)

     # subset: first 10 genes, samples 2, 4, and 10
     expressionSet <- sample.ExpressionSet[1:10,c(2,4,10)]

     # named features and their expression levels
     subset <- expressionSet[c("AFFX-BioC-3_at","AFFX-BioDn-5_at"),]
     exprs(subset)

     # samples with above-average 'score' in phenoData
     highScores <- expressionSet$score > mean(expressionSet$score)
     expressionSet[,highScores]

     # (automatically) coerce to data.frame
     lm(score~AFFX.BioDn.5_at + AFFX.BioC.3_at, data=subset)

