ExpressionSetIllumina {beadarray} | R Documentation

## Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.

### Description

Container for high-throughput assays and experimental metadata. `ExpressionSetIllumina` class is derived from `eSet`, and requires matrices `exprs`, `BeadStDev`, `NoBeads`, `Detection` as assay data members.

### Extends

Directly extends class `eSet`.

### Creating Objects

`new('ExpressionSetIllumina', phenoData = [AnnotatedDataFrame], experimentData = [MIAME], annotation = [character], exprs = [matrix], BeadStDev = [matrix], NoBeads = [matrix], Detection = [matrix], reporterInfo = [data.frameOrNULL], ...)` `ExpressionSetIllumina` instances are usually created through `new("ExpressionSetIllumina", ...)`. Arguments to `new` include `exprs`, `BeadStDev`, `NoBeads`, `Detection`, `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 representing features (e.g., genes) and columns representing samples, a matrix `BeadStDev` describing the standard error of each gene, and matrices `NoBeads` and `Detection` to describe the number of beads used to produce the summary and a probability of a gene being expressed above background. The contents of these matrices are not enforced by the class. Additional matrices of identical size may also be included in `assayData`. Class:`AssayData`
`phenoData`:
  See `eSet`
`experimentData`:
  See `eSet`
`annotation`:
  See `eSet`
`reporterInfo`:
  annotation for SNPs, usually will contain a `CHR` and a `MapInfo` column for genomic localization

### Methods

Class-specific methods:

`exprs(ExpressionSetIllumina)`, `exprs(ExpressionSetIllumina,matrix)<-`
  Access and set elements named `exprs` in the `AssayData` slot.
`se.exprs(ExpressionSetIllumina)`, `se.exprs(ExpressionSetIllumina,matrix)<-`
  Access and set elements named `BeadStDev` in the `AssayData` slot.
`NoBeads(ExpressionSetIllumina)`
  Access elements named `NoBeads` in the `AssayData` slot.
`Detection(ExpressionSetIllumina)`
  Access elements named `Detection` in the `AssayData` slot.
`QCInfo(ExpressionSetIllumina)`
  Access elements named `QC` in the `AssayData` slot.
`object[(index)`:
  Conducts subsetting of matrices and phenoData and reporterInfo components
`combine(ExpressionSetIllumina,ExpressionSetIllumina)`:
  performs `union`-like combination in both dimensions of ExpressionSetIllumina objects
`show(ExpressionSetSetIllumina)`
  See `eSet`
`backgroundNormalise(ExpressionSetIllumina)`
  Normalisation of Illumina data using data from the negative controls on each array stored in the `QC` slot.

Derived from `eSet`:

`sampleNames(ExpressionSetSetIllumina)` and `sampleNames(ExpressionSetSetIllumina)<-`:
  See `eSet`
`featureNames(ExpressionSetSetIllumina)`, `featureNames(ExpressionSetSetIllumina, value)<-`:
  See `eSet`
`dims(ExpressionSetSetIllumina)`:
  See `eSet`
`phenoData(ExpressionSetSetIllumina)`, `phenoData(ExpressionSetSetIllumina,value)<-`:
  See `eSet`
`varLabels(ExpressionSetSetIllumina)`, `varLabels(ExpressionSetSetIllumina, value)<-`:
  See `eSet`
`varMetadata(ExpressionSetSetIllumina)`, `varMetadata(ExpressionSetSetIllumina,value)<-`:
  See `eSet`
`pData(ExpressionSetSetIllumina)`, `pData(ExpressionSetSetIllumina,value)<-`:
  See `eSet`
`varMetadata(ExpressionSetSetIllumina)`, `varMetadata(ExpressionSetSetIllumina,value)`
  See `eSet`
`experimentData(ExpressionSetSetIllumina)`,`experimentData(ExpressionSetSetIllumina,value)<-`:
  See `eSet`
`pubMedIds(ExpressionSetSetIllumina)`, `pubMedIds(ExpressionSetSetIllumina,value)`
  See `eSet`
`abstract(ExpressionSetSetIllumina)`:
  See `eSet`
`annotation(ExpressionSetSetIllumina)`, `annotation(ExpressionSetSetIllumina,value)<-`
  See `eSet`
`storageMode(eSet)`, `storageMode(eSet,character)<-`:
  See `eSet`
`reporterNames(ExpressionSetSetIllumina)`, `reporterNames(ExpressionSetSetIllumina,value)<-`:
  DEPRECATED

Standard generic methods:

`initialize(ExpressionSetSetIllumina)`:
  Object instantiation, used by `new`; not to be called directly by the user.
`validObject(ExpressionSetSetIllumina)`:
  Validity-checking method, ensuring that `call`, `callProbability`, `G`, and `R` are members of `assayData`. `checkValidity(ExpressionSetSetIllumina)` imposes this validity check, and the validity checks of `Biobase:eSet`.
`show(ExpressionSetSetIllumina)`
  See `eSet`
`dim(ExpressionSetSetIllumina)`, `ncol`
  See `eSet`
`ExpressionSetSetIllumina[(index)`:
  See `eSet`
`ExpressionSetSetIllumina$`, `ExpressionSetSetIllumina$<-`
  See `eSet`

### Author(s)

Mark Dunning, based on Biobase eSet class

### See Also

`eSet`

[Package beadarray version 1.4.0 Index]