The caret Package - NexTag Supports Open Source Initiatives

28 normalize.AffyBatch.normalize2Reference
Author(s)
Max Kuhn
Examples
nearZeroVar(iris[, -5], saveMetrics = TRUE)
data(BloodBrain)
nearZeroVar(bbbDescr)
normalize.AffyBatch.normalize2Reference
Quantile Normalization to a Reference Distribution
Description
Quantile normalization based upon a reference distribution. This function normalizes a matrix of
data (typically Affy probe level intensities).
Usage
normalize.AffyBatch.normalize2Reference(
abatch,
type = c("separate", "pmonly", "mmonly", "together"),
ref = NULL)
Arguments
abatch
type
ref
An {AffyBatch}
A string specifying how the normalization should be applied. See details for
more.
A vector of reference values. See details for more.
Details
This method is based upon the concept of a quantile-quantile plot extended to n dimensions. No
special allowances are made for outliers. If you make use of quantile normalization either through
rma or expresso please cite Bolstad et al, Bioinformatics (2003).
The type argument should be one of "separate","pmonly","mmonly","together" which
indicates whether to normalize only one probe type (PM,MM) or both together or separately.
The function uses the data supplied in ref to use as the reference distribution. In other words, the
PMs in abatch will be normalized to have the same distribution as the data in ref. If ref is
NULL, the normalizing takes place using the average quantiles of the PM values in abatch (just
as in normalize.AffyBatch.quantile).