spatial {MANOR} | R Documentation

## 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, gradient
  `arrayCGH` objects before normalization:

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

edge.norm, gradient.norm
  `arrayCGH` 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)

[Package MANOR version 1.14.0 Index]