normalize-methods: Normalize Affymetrix Probe Level Data - methods

In affy: Methods for Affymetrix Oligonucleotide Arrays

Description

Method for normalizing Affymetrix Probe Level Data

Usage

normalize.methods(object)
bgcorrect.methods()
upDate.bgcorrect.methods(x)
pmcorrect.methods()
upDate.pmcorrect.methods(x)

Arguments

object	An AffyBatch.
x	A character vector that will replace the existing one.

Details

If object is an AffyBatch object, then normalize(object) returns an AffyBatch object with the intensities normalized using the methodology specified by getOption("BioC")$affy$normalize.method. The affy package default is quantiles.

Other methodologies can be used by specifying them with the method argument. For example to use the invariant set methodology described by Li and Wong (2001) one would type: normalize(object, method="invariantset").

Further arguments passed by ..., apart from method, are passed along to the function responsible for the methodology defined by the method argument.

A character vector of nicknames for the methodologies available is returned by normalize.methods(object)), where object is an AffyBatch, or simply by typing normalize.AffyBatch.methods. If the nickname of a method is called "loess", the help page for that specific methodology can be accessed by typing ?normalize.loess.

For more on the normalization methodologies currently implemented please refer to the vignette ‘Custom Processing Methods’.

To add your own normalization procedures please refer to the customMethods vignette.

The functions: bgcorrect.methods, pmcorrect.methods, provide access to internal vectors listing the corresponding capabilities.

See Also

AffyBatch-class, normalize.

Examples

if (require(affydata)) {
  data(Dilution)
  normalize.methods(Dilution)
  generateExprSet.methods()
  bgcorrect.methods()
  pmcorrect.methods()
}

Example output

Loading required package: BiocGenerics
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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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

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 connect to server'
Loading required package: affydata
     Package    LibPath                         Item      
[1,] "affydata" "/usr/local/lib/R/site-library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"
[1] "mas"        "methods"    "pmonly"     "subtractmm"

affy documentation built on Nov. 8, 2020, 8:18 p.m.