normalize.quantiles.probeset {affyPLM}R Documentation

Quantile Normalization applied to probesets

Description

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

Usage

  normalize.AffyBatch.quantiles.probeset(abatch,type=c("separate","pmonly","mmonly","together"),use.median=FALSE,use.log=TRUE)

Arguments

abatch An AffyBatch
type how should MM and PM values be handled
use.median use median rather than mean
use.log take logarithms, then normalize

Details

This function applies the quantile method in a probeset specific manner.

In particular a probeset summary is normalized using the quantile method and then the probes adjusted accordingly.

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 Unpublished manuscript http://oz.berkeley.edu/~bolstad/stuff/qnorm.pdf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, normalize.quantiles


[Package affyPLM version 1.6.0 Index]