LumiBatch-class {lumi} | R Documentation

## Class LumiBatch: contain and describe Illumina microarray data

### Description

This is a class representation for Illumina microarray data. It extends `ExpressionSet`.

### Extends

Directly extends class `ExpressionSet`.

### Creating Objects

`new("LumiBatch", exprs = [matrix], se.exprs = [matrix], beadNum = [matrix], detection = [matrix], phenoData = [AnnotatedDataFrame], history = [data.frame], ...)`

`LumiBatch` instances are usually created through `new("LumiBatch", ...)`. The arguments to `new` should include `exprs` and `se.exprs`, others can be missing, in which case they are assigned default values.

Objects can be created using the function `lumiR`.

### Slots

Slot specific to `LumiBatch`:

`history`:

  a data.frame recording the operation history of the LumiBatch object.

`controlData`:

  a data.frame with first two columns as "controlType" and "ProbeID". The rest columns are the control probe expression amplitudes for individual samples.

`QC`:

  a the quality control information of the LumiBatch object, returned by lumiQ function.

Slots inherited from `ExpressionSet`:

`assayData`

  contains equal dimensional matrices: `exprs` (contains gene expression level, which is the mean of its bead replicates.), `se.exprs` (contains gene expression standard error, which is the standard error of its bead replicates.), `beadNum` (records the number of beads for the probe.), `detection` (records the detection p-value of the probe. The number is from [0,1]. By default, < 0.01 indicates good detection.). For more details of `assayData`, please see `ExpressionSet`

`phenoData`:

  See `eSet`

`experimentData`:

  See `eSet`

`annotation`:

  See `eSet`

### Methods

Class-specific methods:

`se.exprs(LumiBatch)`, `se.exprs(LumiBatch,matrix)<-`:

  Access and set elements named `se.exprs` in the `AssayData-class` slot.

`beadNum(LumiBatch)`, `beadNum(LumiBatch)<-`:

  Access and set elements named `beadNum` in the `AssayData-class` slot. Use "beadNum(LumiBatch) <- NULL" to remove the beadNum element.

`detection(LumiBatch)`, `detection(LumiBatch)<-`:

  Access and set elements named `detection` in the `AssayData-class` slot. Use "detection(LumiBatch) <- NULL" to remove the detection element.

`getHistory(LumiBatch)`:

  Access the operation history of `LumiBatch` object.

Derived from `ExpressionSet` (For the directly inherited methods, please see `ExpressionSet` and `eSet`):

`combine(LumiBatch,missing)`:

  Combine two LumiBatch objects, including `history` slot. See `eSet`

`exprs(LumiBatch)`, `exprs(LumiBatch,matrix)<-`:

  Access and set elements named `exprs` in the `AssayData-class` slot.

`object[(i,j)`:

  Conduct subsetting of the data in a LumiBatch object

Standard generic methods (For the directly inherited methods, please see `ExpressionSet` and `eSet`):

`initialize(LumiBatch)`:

  Object instantiation, used by `new`; not to be called directly by the user.

`validObject(LumiBatch)`:

  Validity-checking method, ensuring that `exprs` and `se.exprs` is a member of `assayData`. Other validity check is the same as `checkValidity(ExpressionSet)`.

`show(LumiBatch)`

  A summary of the `LumiBatch` object.

### Author(s)

Pan Du, Simon Lin

### See Also

`lumiR`, `lumiT`, `lumiN`, `boxplot-methods`, `pairs-methods`, `MAplot-methods`

### Examples

    ## load example data
    data(example.lumi)

    ## show the summary of the data
    # summary(example.lumi)
    example.lumi

    ## get expression matrix
    temp <- exprs(example.lumi)

    ## get a subset
    temp <- example.lumi[,1]	## retrieve the first sample

    ## get the probe id
    featureNames(example.lumi)[1:3]

    ## combine LumiBatch objects
    temp <- combine(example.lumi[,1], example.lumi[,3])
    temp

[Package lumi version 2.40.0 Index]