ExpressionSet {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', phenoData = [AnnotatedDataFrame], experimentData = [MIAME], annotation = [character], exprs = [matrix], ...)`

`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`, `experimentData`, and `annotation`. `phenoData`, `experimentData`, and `annotation` 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`
`experimentData`:
  See `eSet`
`annotation`:
  See `eSet`

### Methods

Class-specific methods.

`as(exprSet,"ExpressionSet")`
  Coerce objects of `exprSet-class` to `ExpressionSet`
`exprs(ExpressionSet)`, `exprs(ExpressionSet,matrix)<-`
  Access and set elements named `exprs` in the `AssayData-class` slot.

Derived from `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`
`combine(ExpressionSet,ExpressionSet)`:
  See `eSet`
`storageMode(eSet)`, `storageMode(eSet,character)<-`:
  See `eSet`
`reporterNames(ExpressionSet)`, `reporterNames(ExpressionSet,value)<-`:
  DEPRECATED

Standard generic methods:

`initialize(ExpressionSet)`:
  Object instantiation, used by `new`; not to be called directly by the user.
`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`.
`show(ExpressionSet)`
  See `eSet`
`dim(ExpressionSet)`, `ncol`
  See `eSet`
`ExpressionSet[(index)`:
  See `eSet`
`ExpressionSet$`, `ExpressionSet$<-`
  See `eSet`

### Author(s)

Biocore team

### See Also

`eSet-class`, `ExpressionSet-class`

### Examples

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

    # update existing exprSet-like class to ExpressionSet
    data(sample.exprSet)
    expressionSet <- as(sample.exprSet,"ExpressionSet")
    expressionSet

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

    # subset: first 10 genes, samples 2, 4, and 10
    expressionSet <- as(sample.exprSet,"ExpressionSet")
    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]

[Package Biobase version 1.10.1 Index]