AffyBatch-class {affy} | R Documentation |
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 can be created using the function read.affybatch
or the wrapper ReadAffy
.
cdfName
:character
representing the name of
CDF
file associated with the arrays in the
AffyBatch
.nrow
:integer
representing
the physical number of rows in the arrays.ncol
:integer
representing
the physical number of columns in the arrays.assayData
: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
:AnnotatedDataFrame
containing phenotypic data for the samples.annotation
ExpressionSet
instance.featureData
AnnotatedDataFrame
containing feature-level (e.g., probeset-level) information.experimentData
:notes
:
Class "eSet"
, directly.
signature(object = "AffyBatch")
: Obtains the
cdfName slot.signature(object = "AffyBatch")
: replaces the
perfect match intensities signature(object = "AffyBatch")
: extracts the pm intensities. signature(object = "AffyBatch")
: replaces the
mismatch intensities.signature(object = "AffyBatch")
: extracts the mm intensities. signature(object = "AffyBatch", which)
: extract the
perfect match or mismatch probe intensities. Uses which can be "pm"
and "mm".signature(object = "AffyBatch")
: extracts the
expression matrix.signature(object = "AffyBatch", value = "matrix")
: replaces the
expression matrix.signature(object = "AffyBatch")
: extracts the
matrix of standard errors of expression values, if available.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.signature(x = "AffyBatch")
: creates a
boxplots of log base 2 intensities.
signature(x = "AffyBatch")
: creates a
plot showing all the histograms of the pm,mm or both data. See
plot.density
signature(x = "AffyBatch",
summary.method = "character")
: For each probe set computes an
expression value using summary.method
. 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.signature(object="AffyBatch'")
: deprecated,
use featureNames
signature(object = "AffyBatch")
: retrieve
the environment that defines the location of probes by probe set. signature(x = "AffyBatch")
: creates an image for
each sample.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".
signature(object = "AffyBatch")
: a
replacement method for the exprs
slot, i.e. the intensities. signature(object = "AffyBatch")
: extract the
exprs
slot, i.e. the intensities. signature(x = "AffyBatch")
: returns the number
of samples. signature(object = "AffyBatch")
: return the
location of perfect matches in the intensity matrix.signature(object = "AffyBatch")
: return the
location of the mismatch intensities. signature(x = "AffyBatch")
: Row and column dimensions.signature(x = "AffyBatch")
: An accessor function
for ncol
.signature(x = "AffyBatch")
: an accessor function
for nrow
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).
signature(object = "AffyBatch")
:
returns the normalization methods defined for this class. See normalize
.signature(object = "AffyBatch")
: returns
the probe set associated with each row of the intensity matrix. 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.signature(object = "AffyBatch",
method="character")
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.This class is better described in the vignette.
related methods merge.AffyBatch
,
pairs.AffyBatch
, and
eSet
## 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 eSet sampleNames(affybatch.example) abstract(affybatch.example)