qsplineNormalise {beadarray} | R Documentation

## Qsplinw Normalisation for BeadLevelList objects

### Description

Normalizes expression intensities by fitting a smoothing curves to quantiles

Function is based on the 'normalize.qspline' function in 'affy'

### Usage

    qsplineNormalise(BLData)

### Arguments

`BLData` | can be either an BeadLevelList or BeadSummaryList object

### Details

This normalization method uses the quantiles from each array and the target to fit a system of cubic splines to normalize the data. The target should be the mean (geometric) or median of each probe but could also be the name of a particular chip in the abatch object.

Parameters setting can be of much importance when using this method. The parameter fit.iter is used as a starting point to find a more appropriate value. Unfortunately the algorithm used do not converge in some cases. If this happens, the fit.iter value is used and a warning is thrown. Use of different settings for the parameter samples was reported to give good results. More specifically, for about 200 data points use samples = 0.33, for about 2000 data points use samples = 0.05, for about 10000 data points use samples = 0.02 (thanks to Paul Boutros).

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.

### Value

Produces an BeadLevelList or BeadSummaryList (depending on input type) containing normalised intensity values.

### Author(s)

Laurent and C Workman

### References

Christopher Workman, Lars Juhl Jensen, Hanne Jarmer, Randy Berka, Laurent Gautier, Henrik Bj{o}rn Nielsen, Hans-Henrik Saxild, Claus Nielsen, S{o}ren Brunak, and Steen Knudsen. A new non-linear normal- ization method for reducing variability in dna microarray experiments. Genome Biology, accepted, 2002

### Examples

    data(BLData)

    #BLData.q = qsplineNormalise(BLData)

    #All distributions are fixed to be the same

    #boxplot(log2(BLData.q$R)~col(BLData.q$R))

[Package beadarray version 1.0.0 Index]