| 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)