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. In extends exprSet-class
.
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
:"numeric"
representing
the physical number of rows in the arrays.ncol
:"numeric"
representing
the physical number of columns in the arrays.exprs
:exprSet
. The matrix contains one probe per row and one chip
per column.se.exprs
:exprSet
.phenoData
:exprSet
.annotation
exprSet
instance.description
:characterOrMIAME
has been
defined just for this.notes
:
Class "exprSet"
, 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(x = "AffyBatch")
: replaces subsets. signature(x = "AffyBatch")
: subsets by array.signature(x = "AffyBatch")
: extracts each array as
an Cel
instance.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 geneNames. You must do this by changing
the cdfenvs.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")
: 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")
: 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")
This class is better described in the vignette.
related methods merge.AffyBatch
,
split.AffyBatch
and pairs.AffyBatch
, and related classes Cel
,
Cdf
and
exprSet-class
## 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)