Scale adjust a cDNA Microarray Object

Description

This function loads a maigesRaw or maiges object and scale adjust (normalise between arrays) the data using functions from marray package.

Usage

normScaleMarray(obj=NULL, ...)

Arguments

Details

This function for scale adjustment is entirely based on function maNormScale from marray package. See the help page for this function to see how to set the parameter. Pay attention to the subset argument that is fixed directly from the UseSpots and BadSpots from obj object, and must not be specified in the additional arguments.

The functionality of the scale adjustment function from marray package was added because it uses an estimator of MAD different from that one used in limma package. Also, using maNormScale function it is possible to do print tip scale adjustment.

Value

This function returns a maiges object.

Author(s)

Gustavo H. Esteves <gesteves@vision.ime.usp.br>

See Also

maNormScale from marray package.

Examples

## Loading the dataset
data(gastro)

## Doing global MAD scale adjustment
gastro.norm = normScaleMarray(gastro.norm, norm="globalMAD")
boxplot(gastro.norm) ## To see the effect of MAD adjustment

## For print tip MAD use the following command
## Not run: 
gastro.norm = normScaleMarray(gastro.norm, norm="printTipMAD")

## End(Not run)

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(maigesPack)
Loading required package: convert
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: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: marray
Loading required package: graph
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/maigesPack/normScaleMarray.Rd_%03d_medium.png", width=480, height=480)
> ### Name: normScaleMarray
> ### Title: Scale adjust a cDNA Microarray Object
> ### Aliases: normScaleMarray
> ### Keywords: classes
> 
> ### ** Examples
> 
> ## Loading the dataset
> data(gastro)
> 
> ## Doing global MAD scale adjustment
> gastro.norm = normScaleMarray(gastro.norm, norm="globalMAD")
> boxplot(gastro.norm) ## To see the effect of MAD adjustment
> 
> ## For print tip MAD use the following command
> ## Not run: 
> ##D gastro.norm = normScaleMarray(gastro.norm, norm="printTipMAD")
> ## End(Not run)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>