Background Correction

Description

Background corrects probe intensities in an object of class AffyBatch.

Usage

bg.correct(object, method, ...)

bg.correct.rma(object,...)
bg.correct.mas(object, griddim)
bg.correct.none(object, ...)

Arguments

Details

The name of the method to apply must be double-quoted. Methods provided with the package are currently:

• bg.correct.none: returns object unchanged.

• bg.correct.chipwide: noise correction as described in a ‘white paper’ from Affymetrix.

• bg.correct.rma: the model based correction used by the RMA expression measure.

They are listed in the variable bg.correct.methods. The user must supply the word after "bg.correct", i.e none, subtractmm, rma, etc...

More details are available in the vignette.

R implementations similar in function to the internal implementation used by bg.correct.rma are in bg.adjust.

Value

An AffyBatch for which the intensities have been background adjusted. For some methods (RMA), only PMs are corrected and the MMs remain the same.

Examples

if (require(affydata)) {
  data(Dilution)

  ##bgc will be the bg corrected version of Dilution
  bgc <- bg.correct(Dilution, method="rma") 

  ##This plot shows the tranformation
  plot(pm(Dilution)[,1],pm(bgc)[,1],log="xy",
  main="PMs before and after background correction")
}

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)

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Type 'license()' or 'licence()' for distribution details.

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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(affy)
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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/affy/bgc.Rd_%03d_medium.png", width=480, height=480)
> ### Name: bg.correct
> ### Title: Background Correction
> ### Aliases: bg.correct bg.correct.none bg.correct.rma bg.correct.mas
> ### Keywords: manip
> 
> ### ** Examples
> 
> if (require(affydata)) {
+   data(Dilution)
+ 
+   ##bgc will be the bg corrected version of Dilution
+   bgc <- bg.correct(Dilution, method="rma") 
+ 
+   ##This plot shows the tranformation
+   plot(pm(Dilution)[,1],pm(bgc)[,1],log="xy",
+   main="PMs before and after background correction")
+ }
Loading required package: affydata
     Package    LibPath                            Item      
[1,] "affydata" "/home/ddbj/local/lib64/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"

Warning messages:
1: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'hgu95av2cdf' 
2: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'hgu95av2cdf' 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>