Wrapper functions for vsn

Description

justvsn is equivalent to calling

  fit = vsn2(x, ...)
  nx = predict(fit, newdata=x, useDataInFit = TRUE)

vsnrma is a wrapper around vsn2 and rma.

Usage

justvsn(x, ...)
vsnrma(x, ...)

Arguments

Details

vsnrma does probe-wise background correction and between-array normalization by calling vsn2 on the perfect match (PM) values only. Probeset summaries are calculated with the medianpolish algorithm of rma.

Value

justvsn returns the vsn-normalised intensities in an object generally of the same class as its first argument (see the man page of predict for details). It preserves the metadata.

vsnrma returns an ExpressionSet.

Author(s)

Wolfgang Huber

See Also

vsn2

Examples

##--------------------------------------------------
## use "vsn2" to produce a "vsn" object
##--------------------------------------------------
data("kidney")
fit = vsn2(kidney)
nkid = predict(fit, newdata=kidney)

##--------------------------------------------------
## justvsn on ExpressionSet
##--------------------------------------------------
nkid2 = justvsn(kidney)
stopifnot(identical(exprs(nkid), exprs(nkid2)))

##--------------------------------------------------
## justvsn on RGList
##--------------------------------------------------
rg = new("RGList", list(R=exprs(kidney)[,1,drop=FALSE], G=exprs(kidney)[,2,drop=FALSE]))
erge = justvsn(rg)

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(vsn)
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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/vsn/justvsn.Rd_%03d_medium.png", width=480, height=480)
> ### Name: justvsn
> ### Title: Wrapper functions for vsn
> ### Aliases: justvsn vsnrma
> 
> ### ** Examples
> 
> ##--------------------------------------------------
> ## use "vsn2" to produce a "vsn" object
> ##--------------------------------------------------
> data("kidney")
> fit = vsn2(kidney)
> nkid = predict(fit, newdata=kidney)
> 
> ##--------------------------------------------------
> ## justvsn on ExpressionSet
> ##--------------------------------------------------
> nkid2 = justvsn(kidney)
> stopifnot(identical(exprs(nkid), exprs(nkid2)))
> 
> ##--------------------------------------------------
> ## justvsn on RGList
> ##--------------------------------------------------
> rg = new("RGList", list(R=exprs(kidney)[,1,drop=FALSE], G=exprs(kidney)[,2,drop=FALSE]))
> erge = justvsn(rg)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>