MANOR (version 1.44.0)

qscores: Examples of qscore objects (quality scores) to apply to CGH arrays

Description

This data set provides qscore objects that can be applied to normalized arrayCGH objects in order to evaluate data quality after normalization.

Usage

data(qscores)

Format

The following qscore objects are provided:

	clone.qscore
number of clones
pct.clone.qscore	percentage of clones
	pct.spot.qscore
percentage of spots
pct.spot.before.qscore	percentage of spots before normalization
	pct.replicate.qscore
average percentage of replicates
smoothness.qscore	signal smoothness
	var.replicate.qscore
dyn.x.qscore	signal dynamics on X chromosome
	dyn.y.qscore
signal dynamics on Y chromosome

Source

Institut Curie, .

See Also

spatial, qscore.summary.arrayCGH, qscore

Examples

data(qscores)
data(spatial)

## define a list of qscores
qscore.list <- list(clone=clone.qscore, pct.clone=pct.clone.qscore,
pct.spot=pct.spot.qscore, pct.replicate=pct.replicate.qscore,
smoothness=smoothness.qscore, dyn.x=dyn.x.qscore, dyn.y=dyn.y.qscore,
var.replicate=var.replicate.qscore)

## compute quality scores for a couple of normalized arrays
gradient.norm$quality <- qscore.summary.arrayCGH(gradient.norm,
qscore.list)
print(gradient.norm$quality[, 2:3])

qscore.list$dyn.x$args$test <- 23
qscore.list$dyn.y$args$test <- 24
edge.norm$quality <- qscore.summary.arrayCGH(edge.norm, qscore.list)
print(edge.norm$quality[, 2:3])