Quantile Normalization applied to probesets

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Description

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

Usage

1
  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, bmb@bmbolstad.com

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 Unpublished manuscript http://oz.berkeley.edu/~bolstad/stuff/qnorm.pdf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