normalize.AffyBatch.vsn {vsn} | R Documentation

## Wrapper for vsn to be used as a normalization method with expresso

### Description

Wrapper for `vsn` to be used as a normalization method with the expresso function of the package affy. This is deprecated, plus use `justvsn` instead.

### Usage

    normalize.AffyBatch.vsn(abatch, subsample=20000, niter = 4, strata, ...)

### Arguments

`abatch` | An object of type `AffyBatch`.
`subsample` | The number of probes to be sampled for the fit of the transformation parameters.
`niter` | Parameter passed on to `vsn`.
`strata` | Integer vector of length nrow(y). See `vsn` for details.
`...` | Further parameters for `vsn`.

### Details

Please refer to the "details" and "references" sections of the man page for `vsn` for more details about this method.

Important note: after calling `vsn`, the function `normalize.AffyBatch.vsn` exponentiates the data. This is done in order to make the behavior of this function similar to the other normalization methods in affy. There, it is assumed that in subsequent analysis steps (e.g. in `medpolish`), the logarithm to base 2 needs to be taken.

### Value

An object of class `AffyBatch`.

### Author(s)

Wolfgang Huber http://www.ebi.ac.uk/huber

### See Also

`vsn`

### Examples

    ## Please see vignette.

[Package vsn version 3.2.1 Index]