Last data update: 2014.03.03
R: Quantile Normalization applied to probesets
normalize.quantiles.probeset 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, 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 Unpublished manuscript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
Results