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arrayCGH
and display them
in a convenient way
qscore.summary.arrayCGH(arrayCGH, qscore.list)
arrayCGH
qscore
html.report
for
the generation of an HMTL report of the normalization step.
It can also be used by itself.
qscore
, qscore.summary
, html.report
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])
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