"getdata" <-
function(arraydata) {
# To run ade4 the arraydata needs to be in a data.frame format.
y <- NULL
if (is.matrix(arraydata)) {
if (!is.numeric(arraydata))
stop("Arraydata is a matrix, but is not numeric.")
y <- data.frame(arraydata)
} else if (is.data.frame(arraydata)) {
if (!all(sapply(arraydata, is.numeric)))
stop("Arraydata is a data.frame, but contains non-numeric columns.")
y <- arraydata
} else if ("ExpressionSet" %in% class(arraydata)) {
if (!"affy" %in% rownames(utils::installed.packages()))
stop("affy package is required but not installed. Please install it.")
y <- data.frame(affy::exprs(arraydata))
} else if ("marrayRaw" %in% class(arraydata)) {
nrslides = as.integer(ncol(arraydata@maRf))
nrspots = as.integer(nrow(arraydata@maRf))
tmp = matrix(NA, nrow = nrspots, ncol = 2 * nrslides)
tmp[, (1:nrslides) * 2 - 1] = arraydata@maGf - arraydata@maGb
tmp[, (1:nrslides) * 2] = arraydata@maRf - arraydata@maRb
tmp.names = vector(mode = "character", length = 2 * nrslides)
tmp.names[(1:nrslides) * 2 - 1] = paste("G",colnames(arraydata@maGf),sep="_")
tmp.names[(1:nrslides) * 2] = paste("R",colnames(arraydata@maRf),sep="_")
colnames(tmp) = tmp.names
y <- as.data.frame(tmp)
} else if ("RangedSummarizedExperiment" %in% class(arraydata)) {
y <- SummarizedExperiment::assay(arraydata)
} else {
stop(paste("Arraydata has class ", paste(class(arraydata), sep = ","), ". None is handled.", sep=""))
}
return(y)
}
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