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 |

`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 Unpublished manuscript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

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