normalize.quantiles {affy} | R Documentation |
Using a normalization based upon quantiles, this function normalizes a matrix of probe level intensities.
normalize.quantiles(x,copy=TRUE) normalize.AffyBatch.quantiles(abatch, type=c("separate","pmonly","mmonly","together"))
x |
A matrix of intensities where each column corresponds to a chip and each row is a probe. |
copy |
Make a copy of matrix before normalizing. Usually safer to work with a copy |
abatch |
An AffyBatch |
type |
A string specifying how the normalization should be applied. See details for more. |
This method is based upon the concept of a quantile-quantile
plot extended to n dimensions. No special allowances are made for
outliers. If you make use of quantile normalization either through
rma
or expresso
please cite Bolstad et al, Bioinformatics (2003).
The type arguement should be one of
"separate","pmonly","mmonly","together"
which indicates whether
to normalize only one probe type (PM,MM) or both together or separately.
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 Unpublished manuscript http://oz.berkeley.edu/~bolstad/stuff/qnorm.pdf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