normalize: Normalize an object

In BiocGenerics: S4 generic functions used in Bioconductor

Description

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.

Usage

normalize(object, ...)

Arguments

object	A data object, typically containing microarray data.
...	Additional arguments, for use in specific methods.

Value

An object containing the normalized data.

See Also

• 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.

Examples

normalize
showMethods("normalize")

library(affy)
showMethods("normalize")
selectMethod("normalize", "AffyBatch")

Example output

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"

BiocGenerics documentation built on April 17, 2021, 6:01 p.m.