Examples of array-CGH data with spatial artifacts

Description

This data set provides an example of array-CGH data with spatial artifacts, consisting of including arrayCGH objects before and after normalization

Usage

data(spatial)

Format

• edge, gradientarrayCGH objects before normalization:

  	arrayValues	spot-level information
  	arrayDesign	block design of the array
  	cloneValues	additionnal clone-level data (chromosome, position)

• edge.norm, gradient.normarrayCGH objects after normalization

Details

'edge' presents local spatial bias in the top-right edge corner, and 'gradient' presents global spatial trend. 'edge' and 'gradient' are arrayCGH objects before normalization. They have been created respectively from spot and gpr files using import. 'edge.norm' and 'gradient.norm' are the corresponding arrayCGH objects after normalization using norm.arrayCGH.

flag objects used for data normalization come from flags dataset.

Note

People interested in tools for array-CGH analysis can visit our web-page: http://bioinfo.curie.fr.

Author(s)

Pierre Neuvial, manor@curie.fr.

Source

Institut Curie, manor@curie.fr.

See Also

flags

Examples

data(spatial)

## edge: example of array with local spatial effects

layout(matrix(1:4, 2, 2), height=c(9,1))
arrayPlot(edge, "LogRatio", main="Log-ratios before normalization",
zlim=c(-1,1), bar="h", layout=FALSE, mediancenter=TRUE)
arrayPlot(edge.norm, "LogRatioNorm", main="Log-ratios after spatial
normalization", zlim=c(-1,1), bar="h", layout=FALSE, mediancenter=TRUE) 

## gradient: example of array with spatial gradient

layout(matrix(1:4, 2, 2), height=c(9,1))
arrayPlot(gradient, "LogRatio", main="Log-ratios before normalization",
zlim=c(-2,2), bar="h", layout=FALSE)
arrayPlot(gradient.norm, "LogRatioNorm", main="Log-ratios after spatial
normalization", zlim=c(-2,2), bar="h", layout=FALSE)   

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(MANOR)
Loading required package: GLAD

######################################################################################

Have fun with GLAD

For smoothing it is possible to use either
the AWS algorithm (Polzehl and Spokoiny, 2002,
or the HaarSeg algorithm (Ben-Yaacov and Eldar, Bioinformatics,  2008,

If you use the package with AWS, please cite:
Hupe et al. (Bioinformatics, 2004, and Polzehl and Spokoiny (2002,

If you use the package with HaarSeg, please cite:
Hupe et al. (Bioinformatics, 2004, and (Ben-Yaacov and Eldar, Bioinformatics, 2008,

For fast computation it is recommanded to use
the daglad function with smoothfunc=haarseg

######################################################################################

New options are available in daglad: see help for details.


Attaching package: 'MANOR'

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

    norm

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MANOR/spatial.Rd_%03d_medium.png", width=480, height=480)
> ### Name: spatial
> ### Title: Examples of array-CGH data with spatial artifacts
> ### Aliases: spatial edge edge.norm edge.txt gradient gradient.norm
> ###   gradient.gpr
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(spatial)
> 
> ## edge: example of array with local spatial effects
> 
> layout(matrix(1:4, 2, 2), height=c(9,1))
> arrayPlot(edge, "LogRatio", main="Log-ratios before normalization",
+ zlim=c(-1,1), bar="h", layout=FALSE, mediancenter=TRUE)
> arrayPlot(edge.norm, "LogRatioNorm", main="Log-ratios after spatial
+ normalization", zlim=c(-1,1), bar="h", layout=FALSE, mediancenter=TRUE) 
> 
> ## gradient: example of array with spatial gradient
> 
> layout(matrix(1:4, 2, 2), height=c(9,1))
> arrayPlot(gradient, "LogRatio", main="Log-ratios before normalization",
+ zlim=c(-2,2), bar="h", layout=FALSE)
> arrayPlot(gradient.norm, "LogRatioNorm", main="Log-ratios after spatial
+ normalization", zlim=c(-2,2), bar="h", layout=FALSE)   
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>