Nothing
normalizeAffyBatchqntval <-
function (abatch, type = c("separate", "pmonly", "mmonly", "together"))
{
type <- match.arg(type)
if ((type == "pmonly") | (type == "separate")) {
pms <- unlist(pmindex(abatch))
noNA <- rowSums(is.na(affy::intensity(abatch)[pms, , drop = FALSE])) ==
0
pms <- pms[noNA]
# intensity(abatch)[pms, ] <- normalize.quantiles(intensity(abatch)[pms,
# , drop = FALSE], copy = FALSE)
tmp = normalizeqntval(affy::intensity(abatch)[pms,,drop=FALSE])
affy::intensity(abatch)[pms, ] = tmp$x
Biobase::description(abatch)@preprocessing = c(Biobase::description(abatch)@preprocessing,
list(val=list(method="rma",mqnts=tmp$mqnts)))
}
if ((type == "mmonly") | (type == "separate")) {
mms <- unlist(mmindex(abatch))
noNA <- rowSums(is.na(intensity(abatch)[mms, , drop = FALSE])) ==
0
mms <- mms[noNA]
#intensity(abatch)[mms, ] <- normalize.quantiles(intensity(abatch)[mms,
# , drop = FALSE], copy = FALSE)
tmp = normalizeqntval(affy::intensity(abatch)[mms,,drop=FALSE])
affy::intensity(abatch)[pms, ] = tmp$x
Biobase::description(abatch)@preprocessing = c(Biobase::description(abatch)@preprocessing,
list(val=list(method="rma",mqnts=tmp$mqnts)))
}
if (type == "together") {
pms <- unlist(indexProbes(abatch, "both"))
#intensity(abatch)[pms, ] <- normalize.quantiles(intensity(abatch)[pms,
# , drop = FALSE], copy = FALSE)
tmp = normalizeqntval(affy::intensity(abatch)[mms,,drop=FALSE])
affy::intensity(abatch)[pms, ] = tmp$x
Biobase::description(abatch)@preprocessing = c(Biobase::description(abatch)@preprocessing,
list(val=list(method="rma",mqnts=tmp$mqnts)))
}
return(abatch)
}
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