Generate an expression value from the probes informations

Description

Generate an expression from the probes

Usage

generateExprVal.method.avgdiff(probes, ...)
generateExprVal.method.medianpolish(probes, ...)
generateExprVal.method.liwong(probes, ...)
generateExprVal.method.mas(probes, ...)

Arguments

Value

A list containing entries:

See Also

generateExprSet-methods, generateExprVal.method.playerout, fit.li.wong

Examples

  data(SpikeIn) ##SpikeIn is a ProbeSets
  probes <- pm(SpikeIn) 
  avgdiff <- generateExprVal.method.avgdiff(probes)
  medianpolish <- generateExprVal.method.medianpolish(probes)
  liwong <- generateExprVal.method.liwong(probes)
  playerout <- generateExprVal.method.playerout(probes)
  mas <- generateExprVal.method.mas(probes)
  
  concentrations <- as.numeric(sampleNames(SpikeIn))
  plot(concentrations,avgdiff$exprs,log="xy",ylim=c(50,10000),pch="a",type="b")
  points(concentrations,2^medianpolish$exprs,pch="m",col=2,type="b",lty=2)
  points(concentrations,liwong$exprs,pch="l",col=3,type="b",lty=3)
  points(concentrations,playerout$exprs,pch="p",col=4,type="b",lty=4)
  points(concentrations,mas$exprs,pch="p",col=4,type="b",lty=4)

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 '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
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> 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/generateExprVal.method.avgdiff.Rd_%03d_medium.png", width=480, height=480)
> ### Name: generateExprVal.method.avgdiff
> ### Title: Generate an expression value from the probes informations
> ### Aliases: generateExprVal.method.avgdiff
> ###   generateExprVal.method.medianpolish generateExprVal.method.liwong
> ###   generateExprVal.method.mas
> ### Keywords: manip
> 
> ### ** Examples
> 
>   data(SpikeIn) ##SpikeIn is a ProbeSets
>   probes <- pm(SpikeIn) 
>   avgdiff <- generateExprVal.method.avgdiff(probes)
>   medianpolish <- generateExprVal.method.medianpolish(probes)
>   liwong <- generateExprVal.method.liwong(probes)
>   playerout <- generateExprVal.method.playerout(probes)
>   mas <- generateExprVal.method.mas(probes)
>   
>   concentrations <- as.numeric(sampleNames(SpikeIn))
>   plot(concentrations,avgdiff$exprs,log="xy",ylim=c(50,10000),pch="a",type="b")
>   points(concentrations,2^medianpolish$exprs,pch="m",col=2,type="b",lty=2)
>   points(concentrations,liwong$exprs,pch="l",col=3,type="b",lty=3)
>   points(concentrations,playerout$exprs,pch="p",col=4,type="b",lty=4)
>   points(concentrations,mas$exprs,pch="p",col=4,type="b",lty=4)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>