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]