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. In extends exprSet-class.

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 "numeric" representing the physical number of rows in the arrays.
ncol:
Object of class "numeric" representing the physical number of columns in the arrays.
exprs:
Object of class "matrix" inherited from exprSet. The matrix contains one probe per row and one chip per column.
se.exprs:
Object of class "matrix" inherited from exprSet.
phenoData:
Object of class "phenoData" inherited from exprSet.
annotation
A character string identifying the annotation that may be used for the exprSet instance.
description:
Object of class "MIAME". For compatibility with previous version of this class description can also be a "character". The class characterOrMIAME has been defined just for this.
notes:
Object of class "character" Vector of explanatory text

Extends

Class "exprSet", 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".
[<-
signature(x = "AffyBatch"): replaces subsets.
[
signature(x = "AffyBatch"): subsets by array.
[[
signature(x = "AffyBatch"): extracts each array as an Cel instance.
boxplot
signature(x = "AffyBatch"): creates a boxplots of log base 2 intensities.
hist
signature(x = "AffyBatch"): creates a plot showing all the histograms of the pm,mm or both data. See plot.density
computeExprSet
signature(x = "AffyBatch", summary.method = "character"): For each probe set computes an expression value using summary.method.
geneNames
signature(object = "AffyBatch"): return the probe set names also referred to as the Affymetrix IDs. Notice that one can not assign geneNames. You must do this by changing the cdfenvs.
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.
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.
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.

Note

This class is better described in the vignette.

See Also

related methods merge.AffyBatch, pairs.AffyBatch, and related classes Cel, Cdf and exprSet-class

Examples

## load example
data(affybatch.example)

## nice print
print(affybatch.example)

pm(affybatch.example)[1:5,]
mm(affybatch.example)[1:5,]

## get indexes for the PM probes for the affyID "A28102_at" 
mypmindex <- pmindex(affybatch.example,"A28102_at")
## same operation using the primitive
mypmindex <- indexProbes(affybatch.example, which="pm", genenames="A28102_at")[[1]]
## get the probe intensities from the index
intensity(affybatch.example)[mypmindex, ]

## load bigger example (try 'help(Dilution)' )
data(affybatch.example)
description(affybatch.example) ##we can also use the methods of exprSet
sampleNames(affybatch.example)
abstract(affybatch.example)

[Package affy version 1.8.1 Index]