normalize.quantiles2: Reference quantile normalization

In RefPlus: A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.

Description

Quantile normalization to a reference set.

Usage

normalize.quantiles2(X, Reference.Quantiles)

Arguments

X	A matrix of probe intensity data to be reference quantile normalized.
Reference.Quantiles	A vector of the reference quantiles that the probe intensities of a sample is normalized to.

Details

The function quantile normalized the probe intensities of a set of microarrays to a set of reference quantiles which are formed by a set of reference microarrays.

Value

The reference quantile normalized probe intensities.

Author(s)

Kai-Ming Chang([e-mail])

References

Chang,K.M., Harbron,C., South,M.C. (2006) An Exploration of Extensions to the RMA Algorithm. Available with the RefPlus package.

See Also

normalize.quantiles

Examples

A<-matrix(rnorm(30),10,3)
core<-1:10
An<-normalize.quantiles2(A,core)
rank(A[,1])==An[,1]

Example output

Loading required package: Biobase
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, 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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: affy
Loading required package: affyPLM
Loading required package: gcrma
Loading required package: preprocessCore
Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
 [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE

RefPlus documentation built on Nov. 8, 2020, 5:20 p.m.