normalize.quantiles: Quantile Normalization

Description

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

Usage

normalize.quantiles(x,copy=TRUE)

Arguments

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, but in certain situations not making a copy of the matrix, but instead normalizing it in place will be more memory friendly.

Value

A normalized matrix.

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 please cite Bolstad et al, Bioinformatics (2003).

This functions will handle missing data (ie NA values), based on the assumption that the data is missing at random.

Note that the current implementation optimizes for better memory usage at the cost of some additional run-time.

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 Unpublished manuscript http://bmbolstad.com/stuff/qnorm.pdf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