normalize.contrasts {affy} | R Documentation

## Normalize intensities using the contrasts method

### Description

Scale chip objects in an `AffyBatch-class`.

### Usage

    normalize.AffyBatch.contrasts(abatch,span=2/3, choose.subset=TRUE,
                                  subset.size=5000, verbose=TRUE,
                                  family="symmetric",
                                  type=c("together","pmonly","mmonly","separate"))

### Arguments

`abatch` | an `AffyBatch-class` object.
`span` | parameter to be passed to the function `loess`.
`choose.subset` | Boolean. Defaults to `TRUE`
`subset.size` | Integer. Number of probesets to use in each subset.
`verbose` | verbosity flag.
`family` | parameter to be passed to the function `loess`.
`type` | a string specifying how the normalization should be applied.

### Value

An object of the same class as the one passed.

### See Also

`maffy.normalize`

[Package affy version 1.65.1 Index]