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Last data update: 2014.03.03

R: Background correction of intensity values.

bkgdCorrect

R Documentation

Background correction of intensity values.

Description

Takes a CodelinkSet or Codelink object with Spot mean and Bkgd median values and performes background correction using one of the methods available.

Usage

bkgdCorrect(object, method = "half", preserve = FALSE, verbose = FALSE, offset = 0)

## S4 method for signature 'CodelinkSet'
codCorrect(object, method = "half", normexp.method="saddle", offset=0)

Arguments

`object`	an object of class CodelinkSet or Codelink.
`method`	the correction method to use, one of "none", "subtract", "half" and "normexp".
`preserve`	logical; if Smean and Bmedian slots should be preserved.
`verbose`	logical; if TRUE print some information with method normexp.
`normexp.method`	method used with normexp correction.
`offset`	numeric; value to add to intensities.

Details

Available methods are: . none: left intensities untouched. . subtract: simple subtraction of Bkgd median from Spot mean. . half: the same as above but aboid negative values setting all intensity values below zero to 0.5. . normexp: apply normexp background adjustment from package limma.

Value

An object of class Codelink with corrected intensity values, that is Ri slot.

Author(s)

Diego Diez

Examples

    data(codset)
    codset <- codCorrect(codset, method = "half")

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(codelink)
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

Loading required package: Biobase
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


Attaching package: 'codelink'

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

    plotDensities, plotMA

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

    plotMA

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/codelink/bkgdCorrect.Rd_%03d_medium.png", width=480, height=480)
> ### Name: bkgdCorrect
> ### Title: Background correction of intensity values.
> ### Aliases: bkgdCorrect codCorrect codCorrect,CodelinkSet-method
> ### Keywords: documentation utilities
> 
> ### ** Examples
> 
>     data(codset)
>     codset <- codCorrect(codset, method = "half")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>