pspline {TurboNorm} | R Documentation

## Function for two-colour microarray data normalization using the P-splines

### Description

Wrapper function for two colour microarray data normalization using the P-spline smoother suitable for a RGList- or MarrayRaw-objects.

### Usage

    pspline(object, background = c("none", "substract"), weights = NULL, nintervals = 100, subset=NULL, showArrays = 0, verbose=FALSE, line.col=2,  line.lty=1, line.lwd=2, ...)

### Arguments

`object` | either a RGList or an MarrayRaw-object.
`background` | for background substraction use 'substract'. Default is no backgroud substraction.
`weights` | vector of weights that will be used a for a weighted normalization. The default `NULL` assumse equal weight `1` for all data points.
`nintervals` | number of bins in which the data will be divided. The default is 100 bins.
`showArrays` | either a integer( > 0) or a vector of integers indicating the arrays for which a MA-plot will be produced.
`subset` | subset of the data on which the normalization will be based. A special case of weighted normalization.
`verbose` | if `TRUE` gives additional information on the fit

.

`line.col, line.lty, line.lwd` | line colour, type and width that will be used in the plots, defaults are col=2, lty=1 and lwd=2.
`...` | additional graphical arguments for plotting.

### Details

if necessary?

### Value

The value that will be returned is either a MAList or MarrayNorm-object dependening on the input type.

### Author(s)

Chantal van Leeuwen and Maarten van Iterson

### References

van Iterson M, Duijkers FA, Meijerink JP, Admiraal P, van Ommen GJ, Boer JM, van Noesel MM, Menezes RX (2012). A novel and fast normalization method for high-density arrays. SAGMB, 11(4).

Paul .H.C. Eilers and Brain D. Marx (1996). Flexible smoothing with B-splines and Penalties. Statistical Science, Vol 11, No. 2, 89-121.

### See Also

`normalizeWithinArrays, maNormMain`

### Examples

    library(marray)
    data(swirl)

    x <- pspline(swirl, showArrays=2, pch=20, col="grey")
    x <- pspline(swirl, showArrays=2:4, line.col="green")

[Package TurboNorm version 1.36.0 Index]