normalize.quantiles.probeset: Quantile Normalization applied to probesets
In affyPLM: Methods for fitting probe-level models

Description Usage Arguments Details Value Author(s) References See Also

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

1	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, bmb@bmbolstad.com

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 Unpublished manuscript http://oz.berkeley.edu/~bolstad/stuff/qnorm.pdf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

affyPLM documentation built on Nov. 8, 2020, 6:53 p.m.