lumiN {lumi} | R Documentation |
A main function of between chip normalization of a LumiBatch object. Currently, four methods ("rsn", "ssn", "quantile", "loess", "vsn") are supported.
lumiN(x.lumi, method = c("quantile", "rsn", "ssn", "loess", "vsn"), verbose = TRUE, ...)
x.lumi |
an ExpressionSet inherited object or a data matrix with columns as samples and rows as genes |
method |
four different between chips normalization methods ("quantile", "rsn", "ssn", "loess", "vsn") are supported |
verbose |
a boolean to decide whether to print out some messages |
... |
other parameters used by corresponding method |
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
) and "VSN" (See vsn
). See details in individual functions. Note: the "VSN" normalization should be directly applied to the raw data instead of the lumiT processed data.
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.
Pan Du, Simon Lin
## 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)