MANOR (version 1.44.0)

spatial: 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

Source

Institut Curie, .

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.

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)