Function to apply lowess normalization to an expression set.

Description

Like lnorm, but applies to and returns an ExpressionSet or AffyBatch object instead of a matrix.

Usage

lnormeS(eS, span=0.1)

Arguments

Value

Returns an ExpressionSet with exprs(eS) normalized by lnorm.

Author(s)

John Tillinghast, Blythe Durbin-Johnson

References

http://dmrocke.ucdavis.edu

See Also

lnorm, norm

Examples

library(LMGene)
library(Biobase)

data(sample.eS)

# glog transform expression set
trsample.eS <- transeS (sample.eS, 667, 65)

# normalize expression set
normtrsample.eS <- lnormeS (trsample.eS) 

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> library(LMGene)
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: multtest
Loading required package: survival
Loading required package: affy

Attaching package: 'LMGene'

The following object is masked from 'package:base':

    norm

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/LMGene/lnormeS.Rd_%03d_medium.png", width=480, height=480)
> ### Name: lnormeS
> ### Title: Function to apply lowess normalization to an expression set.
> ### Aliases: lnormeS
> ### Keywords: smooth
> 
> ### ** Examples
> 
> library(LMGene)
> library(Biobase)
> 
> data(sample.eS)
> 
> # glog transform expression set
> trsample.eS <- transeS (sample.eS, 667, 65)
> 
> # normalize expression set
> normtrsample.eS <- lnormeS (trsample.eS) 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>