normalize.quantiles.probeset {affyPLM} | R Documentation |
Using a normalization based upon quantiles, this function normalizes a matrix of probe level intensities.
normalize.AffyBatch.quantiles.probeset(abatch,type=c("separate","pmonly","mmonly","together"),use.median=FALSE,use.log=TRUE)
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 |
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.
A normalized AffyBatch
.
Ben Bolstad, bolstad@stat.berkeley.edu
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 Unpublished manuscript http://oz.berkeley.edu/~bolstad/stuff/qnorm.pdf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
normalize
, normalize.quantiles