normalise {BeadExplorer} | R Documentation

## Normalise a beadData object

### Description

Normalises a beadData object

### Usage

    normalise(beadData, bkd = "Offset", offset = NULL, method = "Quantile", verbose = TRUE, ...)

### Arguments

`beadData` | An object of class `beadData-class`
`bkd` | The background adjustment method to use - "Offset" or "Floor"
`offset` | A number represent the offset constant to use for background adjustment
`method` | The normalisation method to be used - "Quantile", "Qspline", "RobustQuantile" or "None"
`verbose` | Logical, specifying whether commentray shouls be outputted
`...` | Arguments passed to the normalisation function

### Details

Function to normalise a `beadData-class` object. Negative values are removed by the background adjustment option. "Offset" adds a constant to every intensity value - the default is to use the absolute smallest value on the array so that no negative numbers remain. The effect of adding a constant is to reduce the variability at low expression levels. "Floor" sets all expression values less than 0.1 to 0.1. This removes negative values but does not reduce the variability at low expression levels. The normalisation options are from the affy package. See the affy help pages for more information. To use normalised values from the BeadStudio output, select "None" for the normalisation.

### Value

A normalised `beadData-class` object

### Author(s)

Gareth Elvidge gareth.elvidge@well.ox.ac.uk

### References

affy help pages

### See Also

See Also as `help`

### Examples

    data(examplebeadData)
    normdata<-normalise(examplebeadData, bkd="Offset", offset=70, method="Qspline")

[Package BeadExplorer version 1.2.0 Index]