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Last data update: 2014.03.03

R: Function for two-colour microarray data normalization using...

pspline

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.

Examples


library(marray)
data(swirl)

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

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(TurboNorm)
Loading required package: convert
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: marray
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/TurboNorm/pspline.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pspline
> ### Title: Function for two-colour microarray data normalization using the
> ###   P-splines
> ### Aliases: pspline
> ### Keywords: smooth
> 
> ### ** Examples
> 
> 
> library(marray)
> data(swirl)
> 
> x <- pspline(swirl, showArrays=2, pch=20, col="grey")
> x <- pspline(swirl, showArrays=2:4, line.col="green")
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>