lumiN: Between chip normalization of a LumiBatch object

In lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

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)

lumi documentation built on Nov. 8, 2020, 5:27 p.m.