AffyBatch-class {affy} | R Documentation

## Class AffyBatch

### Description

This is a class representation for Affymetrix GeneChip probe level data. The main component are the intensities from multiple arrays of the same `CDF` type. It extends `eSet`.

### Objects from the Class

Objects can be created using the function `read.affybatch` or the wrapper `ReadAffy`.

### Slots

`cdfName`:
  Object of class `character` representing the name of `CDF` file associated with the arrays in the `AffyBatch`.
`nrow`:
  Object of class `integer` representing the physical number of rows in the arrays.
`ncol`:
  Object of class `integer` representing the physical number of columns in the arrays.
`assayData`:
  Object of class `AssayData` containing the raw data, which will be at minimum a matrix of intensity values. This slot can also hold a matrix of standard errors if the 'sd' argument is set to `TRUE` in the call to `ReadAffy`.
`phenoData`:
  Object of class `AnnotatedDataFrame` containing phenotypic data for the samples.
`annotation`
  A character string identifying the annotation that may be used for the `ExpressionSet` instance.
`featureData`
  Object of class `AnnotatedDataFrame` containing feature-level (e.g., probeset-level) information.
`experimentData`:
  Object of class "MIAME" containing experiment-level information.
`notes`:
  Object of class "character" Vector of explanatory text

### Extends

Class `"eSet"`, directly.

### Methods

cdfName
  `signature(object = "AffyBatch")`: Obtains the cdfName slot.
pm<-
  `signature(object = "AffyBatch")`: replaces the perfect match intensities
pm
  `signature(object = "AffyBatch")`: extracts the pm intensities.
mm<-
  `signature(object = "AffyBatch")`: replaces the mismatch intensities.
mm
  `signature(object = "AffyBatch")`: extracts the mm intensities.
probes
  `signature(object = "AffyBatch", which)`: extract the perfect match or mismatch probe intensities. Uses which can be "pm" and "mm".
exprs
  `signature(object = "AffyBatch")`: extracts the expression matrix.
exprs<-
  `signature(object = "AffyBatch", value = "matrix")`: replaces the expression matrix.
se.exprs
  `signature(object = "AffyBatch")`: extracts the matrix of standard errors of expression values, if available.
se.exprs<-
  `signature(object = "AffyBatch", value = "matrix")`: replaces the matrix of standard errors of expression values.
[<-
  `signature(x = "AffyBatch")`: replaces subsets.
[
  `signature(x = "AffyBatch")`: subsets by array.
boxplot
  `signature(x = "AffyBatch")`: creates a `boxplots of log base 2 intensities (pm, mm or both). Defaults to both.`
hist
  `signature(x = "AffyBatch")`: creates a plot showing all the histograms of the pm,mm or both data. See `plotDensity`
computeExprSet
  `signature(x = "AffyBatch", summary.method = "character")`: For each probe set computes an expression value using `summary.method`.
featureNames
  `signature(object = "AffyBatch")`: return the probe set names also referred to as the Affymetrix IDs. Notice that one can not assign `featureNames`. You must do this by changing the cdfenvs.
geneNames
  `signature(object="AffyBatch'")`: deprecated, use `featureNames`
getCdfInfo
  `signature(object = "AffyBatch")`: retrieve the environment that defines the location of probes by probe set.
image
  `signature(x = "AffyBatch")`: creates an image for each sample.
indexProbes
  `signature(object = "AffyBatch", which = "character")`: returns a list with locations of the probes in each probe set. The affyID corresponding to the probe set to retrieve can be specified in an optional parameter `genenames`. By default, all the affyIDs are retrieved. The names of the elements in the list returned are the affyIDs. `which` can be "pm", "mm", or "both". If "both" then perfect match locations are given followed by mismatch locations.

  `signature(object = "AffyBatch", which = "missing")` (i.e., calling `indexProbes` without a "which" argument) is the same as setting "which" to "pm".

intensity<-
  `signature(object = "AffyBatch")`: a replacement method for the `exprs` slot, i.e. the intensities.
intensity
  `signature(object = "AffyBatch")`: extract the `exprs` slot, i.e. the intensities.
length
  `signature(x = "AffyBatch")`: returns the number of samples.
pmindex
  `signature(object = "AffyBatch")`: return the location of perfect matches in the intensity matrix.
mmindex
  `signature(object = "AffyBatch")`: return the location of the mismatch intensities.
dim
  `signature(x = "AffyBatch")`: Row and column dimensions.
ncol
  `signature(x = "AffyBatch")`: An accessor function for `ncol`.
nrow
  `signature(x = "AffyBatch")`: an accessor function for `nrow`
.
normalize
  `signature(object = "AffyBatch")`: a method to `normalize`. The method accepts an argument `method`. The default methods is specified in package options (see the main vignette).
normalize.methods
  `signature(object = "AffyBatch")`: returns the normalization methods defined for this class. See `normalize`.
probeNames
  `signature(object = "AffyBatch")`: returns the probe set associated with each row of the intensity matrix.
probeset
  `signature(object = "AffyBatch",genenames=NULL, locations=NULL)`: Extracts `ProbeSet` objects related to the probe sets given in genenames. If an alternative set of locations defining pms and mms a list with those locations should be passed via the `locations` argument.
bg.correct
  `signature(object = "AffyBatch", method="character")`
applies background correction methods defined by method.
updateObject
  `signature(object = "AffyBatch", ..., verbose=FALSE)`: update, if necessary, an object of class AffyBatch to its current class definition. `verbose=TRUE` provides details about the conversion process.

### Note

This class is better described in the vignette.

### See Also

related methods `merge.AffyBatch`, `pairs.AffyBatch`, and `eSet`

### Examples

    if (require(affydata)) {
      ## load example
      data(Dilution)

      ## nice print
      print(Dilution)

      pm(Dilution)[1:5,]
      mm(Dilution)[1:5,]

      ## get indexes for the PM probes for the affyID "1900_at"
      mypmindex <- pmindex(Dilution,"1900_at")
      ## same operation using the primitive
      mypmindex <- indexProbes(Dilution, which="pm", genenames="1900_at")[[1]]
      ## get the probe intensities from the index
      intensity(Dilution)[mypmindex, ]

      description(Dilution) ##we can also use the methods of eSet
      sampleNames(Dilution)
      abstract(Dilution)
    }

[Package affy version 1.22.1 Index]