Last data update: 2014.03.03

R: Between chip normalization of a LumiBatch object
lumiNR Documentation

Between chip normalization of a LumiBatch object

Description

A main function of between chip normalization of a LumiBatch object. Currently, four methods ("rsn", "ssn", "quantile", "loess", "vsn") are supported.

Usage

lumiN(x.lumi, method = c("quantile", "rsn", "ssn", "loess", "vsn", "rankinvariant"), verbose = TRUE, ...)

Arguments

x.lumi

an ExpressionSet inherited object or a data matrix with columns as samples and rows as genes

method

five different between chips normalization methods ("quantile", "rsn", "ssn", "loess", "vsn", "rankinvariant") are supported

verbose

a boolean to decide whether to print out some messages

...

other parameters used by corresponding method

Details

lumiN is an interface for different normalization methods. Currently it supports "RSN" (See rsn), "SSN" (See ssn), "loess" (See normalize.loess), "quantile" (See normalize.quantiles), "VSN" (See vsn) and "rankinvariant" (See rankinvariant) . See details in individual functions. Note: the "VSN" normalization should be directly applied to the raw data instead of the lumiT processed data.

Value

Return an object with expression values normalized. The class of the return object is the same as the input object x.lumi. If it is a LumiBatch object, it also includes the VST transform function and its parameters as attributes: "transformFun", "parameter". See inverseVST for details.

Author(s)

Pan Du, Simon Lin

See Also

rsn, ssn, rankinvariant

Examples

## load example data
data(example.lumi)

## Do lumi transform
lumi.T <- lumiT(example.lumi)

## Do lumi between chip normaliazation
lumi.N <- lumiN(lumi.T, method='rsn', ifPlot=TRUE)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(lumi)
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, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

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

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/lumi/lumiN.Rd_%03d_medium.png", width=480, height=480)
> ### Name: lumiN
> ### Title: Between chip normalization of a LumiBatch object
> ### Aliases: lumiN
> ### Keywords: methods
> 
> ### ** Examples
> 
> ## load example data
> data(example.lumi)
> 
> ## Do lumi transform
> lumi.T <- lumiT(example.lumi)
Perform vst transformation ...
2016-07-06 21:29:11 , processing array  1 
2016-07-06 21:29:11 , processing array  2 
2016-07-06 21:29:11 , processing array  3 
2016-07-06 21:29:12 , processing array  4 
> 
> ## Do lumi between chip normaliazation
> lumi.N <- lumiN(lumi.T, method='rsn', ifPlot=TRUE)
Perform rsn normalization ...
2016-07-06 21:29:12 , processing array  1 
2016-07-06 21:29:12 , processing array  2 
2016-07-06 21:29:12 , processing array  3 
2016-07-06 21:29:12 , processing array  4 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>