LESN - Low End Signal is Noise Background corrections

Description

This function background corrects PM probe data using LESN - Low End Signal is Noise concepts.

Usage

bg.correct.LESN(object, method=2, baseline=0.25, theta=4)

Arguments

Details

This method will be more formally documented at a later date.

The basic concept is to consider that the lowest end of intensites is most likely just noise (and should be heavily corrected) and the highest end signals are most likely signal and should have little adjustment. Low end signals are made much smaller while high end signals get less adjustment relative adjustment.

Value

An AffyBatch

Author(s)

Ben Bolstad bmb@bmbolstad.com

References

Bolstad, BM (2004) Low Level Analysis of High-density Oligonucleotide Array Data: Background, Normalization and Summarization. PhD Dissertation. University of California, Berkeley.

Examples

if (require(affydata)) {
  data(Dilution)
  Dilution.example.bgcorrect <- bg.correct.LESN(Dilution)
}

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(affyPLM)
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: affy
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: gcrma
Loading required package: preprocessCore
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/affyPLM/bg.correct.LESN.Rd_%03d_medium.png", width=480, height=480)
> ### Name: bg.correct.LESN
> ### Title: LESN - Low End Signal is Noise Background corrections
> ### Aliases: bg.correct.LESN
> ### Keywords: manip
> 
> ### ** Examples
> 
> if (require(affydata)) {
+   data(Dilution)
+   Dilution.example.bgcorrect <- bg.correct.LESN(Dilution)
+ }
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 
>