spatial {MANOR} | R Documentation |
This data set provides an example of array-CGH data with spatial
artifacts, consisting of including arrayCGH
objects before and after normalization
data(spatial)
arrayCGH
objects before normalization:
arrayValues | spot-level information | |
arrayDesign | block design of the array | |
cloneValues | additionnal clone-level data (chromosome, position) |
arrayCGH
objects after normalization
'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.
People interested in tools for array-CGH analysis can visit our web-page: http://bioinfo.curie.fr.
Pierre Neuvial, manor@curie.fr.
Institut Curie, manor@curie.fr.
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)