# normalize.AffyBatch.normalize2Reference

##### Quantile Normalization to a Reference Distribution

Quantile normalization based upon a reference distribution. This function normalizes a matrix of data (typically Affy probe level intensities).

- Keywords
- manip

##### Usage

```
normalize.AffyBatch.normalize2Reference(
abatch,
type = c("separate", "pmonly", "mmonly", "together"),
ref = NULL)
```

##### Arguments

- abatch
- An
`{AffyBatch}`

- type
- A string specifying how the normalization should be applied. See details for more.
- ref
- A vector of reference values. See details for more.

##### Details

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 argument should be one of
`"separate","pmonly","mmonly","together"`

which indicates whether
to normalize only one probe type (PM,MM) or both together or separately.
The function uses the data supplied in `ref`

to use as the reference
distribution. In other words, the PMs in `abatch`

will be normalized
to have the same distribution as the data in `ref`

. If `ref`

is
`NULL`

, the normalizing takes place using the average quantiles
of the PM values in `abatch`

(just as in `normalize.AffyBatch.quantile`

).

##### Value

- A normalized
`AffyBatch`

.

##### References

Bolstad, B (2001) *Probe Level Quantile Normalization of High Density
Oligonucleotide Array Data*. Unpublished manuscript

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.

##### See Also

`normalize`

##### Examples

```
# first, let affy/expresso know that the method exists
# normalize.AffyBatch.methods <- c(normalize.AffyBatch.methods, "normalize2Reference")
# example not run, as it would take a while
# RawData <- ReadAffy(celfile.path=FilePath)
# Batch1Step1 <- bg.correct(RawData, "rma")
# Batch1Step2 <- normalize.AffyBatch.quantiles(Batch1Step1)
# referencePM <- pm(Batch1Step2)[,1]
# Batch1Step3 <- computeExprSet(Batch1Step2, "pmonly", "medianpolish")
# Batch2Step1 <- bg.correct(RawData2, "rma")
# Batch2Step2 <- normalize.AffyBatch.normalize2Reference(Batch2Step1, ref = referencePM)
# Batch2Step3 <- computeExprSet(Batch2Step2, "pmonly", "medianpolish")
```

*Documentation reproduced from package caret, version 4.41, License: GPL-2*