Nothing
"normalize.AffyBatch.normalize2Reference" <-
function (abatch, type = c("separate", "pmonly", "mmonly", "together"), ref = NULL)
{
type <- match.arg(type)
if ((type == "pmonly") | (type == "separate")) {
pms <- unlist(pmindex(abatch))
noNA <- rowSums(is.na(intensity(abatch)[pms, , drop = FALSE])) == 0
pms <- pms[noNA]
intensity(abatch)[pms, ] <- normalize2Reference(
intensity(abatch)[pms, , drop = FALSE],
refData = ref, ties = TRUE)
}
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, ] <- normalize2Reference(
intensity(abatch)[mms, , drop = FALSE],
refData = ref, ties = TRUE)
}
if (type == "together") {
pms <- unlist(indexProbes(abatch, "both"))
intensity(abatch)[pms, ] <- normalize2Reference(
intensity(abatch)[pms, , drop = FALSE],
refData = ref, ties = TRUE)
}
return(abatch)
}
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