Last data update: 2014.03.03

R: Li Wong rank / invariant probeset normalization
LiWongRankR Documentation

Li Wong rank / invariant probeset normalization

Description

Performs a Li Wong rank / invariant probeset normalization (see References).

Usage

LiWongRank(header, dataset, listOfArgs)

Arguments

header

the header of a dataset file generated with generateDatasetFile

dataset

an R data frame generated with generateDatasetFile

listOfArgs

a list containing:

- a character string specifying the column whose values will be used for normalization

- a character string specifying the name of the dataset column to be used for the computation of the siRNA/gene ranks

Details

For each plate type/layout in each experiment, generates a ranked list of siRNAs according to their intensity values. Only siRNAs occuring only once on the plate are allowed in the list. The normalization is performed only if all plate types have a maximum of 20

For each "unique" siRNA on a plate type, the variance of its ranks across plates is computed. A histogram of variances is plotted and allows the user to choose a threshold. A list of siRNAs with rank variances under the given threshold is then returned for each plate type so that the user can choose an siRNA to normalize the plate with.

Value

Returns a list containing:

header

the new header (with an added entry about the normalization procedure in the comments)

dataset

the new dataset with normalized values. The old values are saved in an extra column with the suffix ".old"

References

C. Li and WH Wong. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol, 2(8):research0032.1-0032.11, 2001.

E. Schadt, C. Li, B. Ellis, and WH Wong. Feature Extraction and Normalization Algorithms for High-Density Oligonucleotide Gene Expression Array Data. J Cell Biochem Suppl, 37:120-125, 2001.

Examples

data(exampleHeader, package="RNAither")
data(exampleDataset, package="RNAither")

normres <- LiWongRank(header, dataset, list("SigIntensity", "GeneName"))
newheader=normres[[1]]
newdataset=normres[[2]]

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(RNAither)
Loading required package: topGO
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: graph
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: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums


Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

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

    members

Loading required package: RankProd
Loading required package: prada
Loading required package: RColorBrewer
Loading required package: grid

Attaching package: 'grid'

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

    depth

Loading required package: rrcov
Loading required package: robustbase

Attaching package: 'robustbase'

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

    rowMedians

Scalable Robust Estimators with High Breakdown Point (version 1.3-11)


Attaching package: 'RNAither'

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

    trim

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RNAither/LiWongRank.Rd_%03d_medium.png", width=480, height=480)
> ### Name: LiWongRank
> ### Title: Li Wong rank / invariant probeset normalization
> ### Aliases: LiWongRank
> ### Keywords: manip
> 
> ### ** Examples
> 
> data(exampleHeader, package="RNAither")
> data(exampleDataset, package="RNAither")
> 
> normres <- LiWongRank(header, dataset, list("SigIntensity", "GeneName"))
      c1       c2 
 [1,] NA       NA 
 [2,] NA       NA 
 [3,] "FGF17"  "0"
 [4,] "SULF1"  "0"
 [5,] "CCNL2"  "0"
 [6,] "ATP1A1" "0"
 [7,] "STK36"  "0"
 [8,] "CGNR"   "0"
 [9,] "GABRA1" "0"
[10,] "STK39"  "0"
     c1      c2                 
[1,] NA      NA                 
[2,] NA      NA                 
[3,] "PGSR"  "0"                
[4,] "LRRC6" "0.707106781186548"
[5,] "GJA4"  "1.4142135623731"  
> newheader=normres[[1]]
> newdataset=normres[[2]]
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>