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Last data update: 2014.03.03

R: Scaling normalization

normalize.scaling

R Documentation

Scaling normalization

Description

Allows the user to apply scaling normalization.

Usage

normalize.scaling(X,trim=0.02, baseline=-1, log.scalefactors=FALSE)
normalize.AffyBatch.scaling(abatch,
    type=c("together","pmonly","mmonly","separate"),
    trim=0.02, baseline=-1, log.scalefactors=FALSE)

Arguments

`X`	A matrix. The columns of which are to be normalized.
`abatch`	An `AffyBatch`
`type`	A parameter controlling how normalization is applied to the Affybatch.
`trim`	How much to trim from the top and bottom before computing the mean when using the scaling normalization.
`baseline`	Index of array to use as baseline, negative values (-1,-2,-3,-4) control different baseline selection methods.
`log.scalefactors`	Compute the scale factors based on log2 transformed data.

Details

These function carries out scaling normalization of expression values.

Value

A normalized ExpressionSet.

Author(s)

Ben Bolstad, bmb@bmbolstad.com

Examples

if (require(affydata)) {
  data(Dilution)
  normalize.AffyBatch.scaling(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.
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'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/normalize.scaling.Rd_%03d_medium.png", width=480, height=480)
> ### Name: normalize.scaling
> ### Title: Scaling normalization
> ### Aliases: normalize.scaling normalize.AffyBatch.scaling
> ### Keywords: manip
> 
> ### ** Examples
> 
> if (require(affydata)) {
+   data(Dilution)
+   normalize.AffyBatch.scaling(Dilution)
+ }
Loading required package: affydata
     Package    LibPath                            Item      
[1,] "affydata" "/home/ddbj/local/lib64/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"

AffyBatch object
size of arrays=640x640 features (35221 kb)
cdf=HG_U95Av2 (12625 affyids)
number of samples=4
number of genes=12625
annotation=hgu95av2
notes=
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 
>