Lowess normalization function

Description

Lowess normalization function

Usage

lnorm(mat1, span = 0.1)

Arguments

Details

mat1 must be a p by n matrix, where p is the number of genes and n is the number of arrays or samples

Value

Author(s)

David Rocke and Geun-Cheol Lee

References

http://dmrocke.ucdavis.edu

See Also

lnormeS, norm

Examples

library(Biobase)
library(LMGene)

#data
data(sample.mat)
data(vlist)

raw.eS <- neweS(sample.mat, vlist)

# glog transform data
trans.eS <- transeS(raw.eS, lambda = 727, alpha = 56)

# normalize
normed.exprs <- lnorm(exprs(trans.eS))

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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'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(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/lnorm.Rd_%03d_medium.png", width=480, height=480)
> ### Name: lnorm
> ### Title: Lowess normalization function
> ### Aliases: lnorm
> ### Keywords: smooth
> 
> ### ** Examples
> 
> library(Biobase)
> library(LMGene)
> 
> #data
> data(sample.mat)
> data(vlist)
> 
> raw.eS <- neweS(sample.mat, vlist)
> 
> # glog transform data
> trans.eS <- transeS(raw.eS, lambda = 727, alpha = 56)
> 
> # normalize
> normed.exprs <- lnorm(exprs(trans.eS))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>