Background correction

Description

Background correction based on backgroundCorrect of the limma package.

Usage

backgroundCorrect2(object,method="subtract", offset=0)

Arguments

Details

This function is a wrapper function for backgroundCorrect with following methods implemented:

• “none”: no background correction

• “subtract”: simple subtraction of background intensities

• “movingmin”: background intensities are first averaged over 3x3 grids of neighbouring spots and subsequently substracted

• “minimum”: zero or negative intensities after background correction are set equal to half the minimum of positive corrected intensities

• “edwards”: background correction based on log-linear interpolation

• “normexp”: background correction based on fitting procedure

For further details and references, please refer to its help page. An alternative Bayesian model for background correction (kooperberg) is also implemented in the limma package.

Value

Background correct object of class marrayRaw.

Author(s)

Matthias Futschik

See Also

backgroundCorrect,kooperberg

Examples

# Loading data
data(sw)

#No background correction
  sw.none <- backgroundCorrect2(sw,method="none")
  plot(maA(sw.none)[,1],maM(sw.none)[,1])

# Simple subtraction
  sw.sub <- backgroundCorrect2(sw,method="sub")
  points(maA(sw.sub)[,1],maM(sw.sub)[,1],col="red")
 

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(OLIN)
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: marray
Loading required package: limma
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/OLIN/backgroundCorrect2.Rd_%03d_medium.png", width=480, height=480)
> ### Name: backgroundCorrect2
> ### Title: Background correction
> ### Aliases: backgroundCorrect2
> ### Keywords: utilities
> 
> ### ** Examples
> 
> 
> # Loading data
> data(sw)
> 
> #No background correction
>   sw.none <- backgroundCorrect2(sw,method="none")
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 object is masked from 'package:limma':

    plotMA

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")'.

>   plot(maA(sw.none)[,1],maM(sw.none)[,1])
> 
> # Simple subtraction
>   sw.sub <- backgroundCorrect2(sw,method="sub")
>   points(maA(sw.sub)[,1],maM(sw.sub)[,1],col="red")
>  
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>