Description Usage Arguments Value See Also Examples
A generic function which normalizes an object containing microarray data or other data. Normalization is intended to remove from the intensity measures any systematic trends which arise from the microarray technology rather than from differences between the probes or between the target RNA samples hybridized to the arrays.
1 |
object |
A data object, typically containing microarray data. |
... |
Additional arguments, for use in specific methods. |
An object containing the normalized data.
showMethods
for displaying a summary of the
methods defined for a given generic function.
selectMethod
for getting the definition of
a specific method.
normalize,AffyBatch-method in the affy
package and normalize,MSnExp-method in the
MSnbase package for examples of specific normalize
methods (defined for AffyBatch and
MSnExp objects, respectively).
BiocGenerics for a summary of all the generics defined in the BiocGenerics package.
1 2 3 4 5 6 | normalize
showMethods("normalize")
library(affy)
showMethods("normalize")
selectMethod("normalize", "AffyBatch")
|
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
standardGeneric for "normalize" defined from package "BiocGenerics"
function (object, ...)
standardGeneric("normalize")
<environment: 0x2feb658>
Methods may be defined for arguments: object
Use showMethods("normalize") for currently available ones.
Function: normalize (package BiocGenerics)
<No methods>
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Warning message:
In read.dcf(con) :
URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
Function: normalize (package BiocGenerics)
object="AffyBatch"
Method Definition:
function (object, ...)
{
.local <- function (object, method = getOption("BioC")$affy$normalize.method,
...)
{
method <- match.arg(method, normalize.AffyBatch.methods())
if (is.na(method))
stop("unknown method")
method <- paste("normalize.AffyBatch", method, sep = ".")
object <- do.call(method, alist(object, ...))
preproc <- c(description(object)@preprocessing, list(normalization = attr(object,
"normalization")))
attr(object, "normalization") <- NULL
MIAME <- description(object)
MIAME@preprocessing <- preproc
description(object) <- MIAME
return(object)
}
.local(object, ...)
}
<environment: namespace:affy>
Signatures:
object
target "AffyBatch"
defined "AffyBatch"
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