affy: normalize.quantiles – R documentation

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affy

normalize.quantiles

Quantile Normalization

Description

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

Usage

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

Arguments

`abatch`	an `AffyBatch` object.
`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 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.

Value

A normalized AffyBatch.

Author(s)

Ben Bolstad, bmbolstad.com

References

Bolstad, B (2001) Probe Level Quantile Normalization of High Density Oligonucleotide Array Data. Unpublished manuscript http://bmbolstad.com/stuff/qnorm.pdf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://bmbolstad.com/misc/normalize/normalize.html