CDF type. It extends
eSet.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.annotationExpressionSet
instance.protocolData:AnnotatedDataFrame
containing protocol data for the samples.featureDataAnnotatedDataFrame
containing feature-level (e.g., probeset-level) information.experimentData:.__classVersion__:Versions
describing the R and Biobase version number used to create the
instance. Intended for developer use."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 (pm, mm or both).
Defaults to both.signature(x = "AffyBatch"): creates a plot showing
all the histograms of the pm,mm or both data. See
plotDensity.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") applies background correction methods defined by
method.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.merge.AffyBatch,
pairs.AffyBatch, and
eSetif (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)
}
Run the code above in your browser using DataLab