normalize.quantiles {affy}R Documentation

Quantile Normalization

Description

Using a normalization based upon quantiles, this function normalizes a matrix of probe level intensities.

Usage

  normalize.quantiles(x,copy=TRUE)
  normalize.AffyBatch.quantiles(abatch, type=c("separate","pmonly","mmonly","together"))

Arguments

x A matrix of intensities where each column corresponds to a chip and each row is a probe.
copy Make a copy of matrix before normalizing. Usually safer to work with a copy
abatch An AffyBatch
type A string specifying how the normalization should be applied. 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 arguement should be one of "separate","pmonly","mmonly","together" which indicates whether to normalize only one probe type (PM,MM) or both together or separately.

Value

A normalized AffyBatch.

Author(s)

Ben Bolstad, bolstad@stat.berkeley.edu

References

Bolstad, B (2001) Probe Level Quantile Normalization of High Density Oligonucleotide Array Data. Unpublished manuscript http://oz.berkeley.edu/~bolstad/stuff/qnorm.pdf

Bolstad, B. M., Irizarry R. A., Astrand, M, and Speed, T. P. (2003) A Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Bias and Variance. Bioinformatics 19(2) ,pp 185-193. http://www.stat.berkeley.edu/~bolstad/normalize/normalize.html

See Also

normalize


[Package affy version 1.8.1 Index]