Fitting a RMA model

Description

Obtain reference quantiles and reference probe effects based on reference set Train, and calculate the gene expression

Usage

rma.para(Train, bg = TRUE, exp = FALSE)

Arguments

Value

Note

The RMA procedure requires a lot of computer memory.

Author(s)

Kai-Ming Chang(kaiming@gmail.com)

References

Chang,K.M., Harbron,C., South,M.C. (2006) An Exploration of Extensions to the RMA Algorithm. Available with the RefPlus package.

See Also

rmaplus,rmaref.predict

Examples

if (require(affydata)) {
  ## Use Dilution in affydata package
  data(Dilution)

  ## Background correct, estimate the probe effects, and calculate the 
  ## RMA intensities using rma.para function.
  Ex<-rma.para(Dilution, bg=TRUE,exp=TRUE)

  ## Calculate the rma intensities using rma function.
  Ex0<-exprs(rma(Dilution))

  plot(Ex$express[,1],Ex0[,1])
}

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 'demo()' for some demos, 'help()' for on-line help, or
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> library(RefPlus)
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 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")'.

Loading required package: affy
Loading required package: affyPLM
Loading required package: gcrma
Loading required package: preprocessCore
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RefPlus/rma.para.Rd_%03d_medium.png", width=480, height=480)
> ### Name: rma.para
> ### Title: Fitting a RMA model
> ### Aliases: rma.para
> ### Keywords: manip
> 
> ### ** Examples
> 
> if (require(affydata)) {
+   ## Use Dilution in affydata package
+   data(Dilution)
+ 
+   ## Background correct, estimate the probe effects, and calculate the 
+   ## RMA intensities using rma.para function.
+   Ex<-rma.para(Dilution, bg=TRUE,exp=TRUE)
+ 
+   ## Calculate the rma intensities using rma function.
+   Ex0<-exprs(rma(Dilution))
+ 
+   plot(Ex$express[,1],Ex0[,1])
+ }
Loading required package: affydata
     Package    LibPath                            Item      
[1,] "affydata" "/home/ddbj/local/lib64/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"

Background correcting
Normalizing
Calculating Expression
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 
>