[BioC] edgeR plotMDS.DGEList() use of normalized counts
Ted Toal [guest]
guest at bioconductor.org
Sat Nov 10 00:51:52 CET 2012
When an MDS plot is made using plotMDS.DGEList(), if the DGEList object that is supplied as an argument contains normalization factors, are they used to make the MDS plot? I'm told that they are, and yet when I look at the function code, it appears that unnormalized raw counts are being internally normalized in the function without using the normalization factors present in the DGEList object. I'm pasting the relevant code from plotMDS.DGEList() below. I don't see any use of x$samples$lib.size or x$samples$norm.factors, which contain the normalization factors, within the function.
-- output of sessionInfo():
subdata <- x$counts[o, ]
gm <- function(x) exp(mean(log(x)))
myFun <- function(delta, y, ...) colSums(condLogLikDerDelta(y,
delta, ...))
for (i in 2:(nsamples)) {
for (j in 1:(i - 1)) {
mm <- subdata[, c(i, j)]
rs5 <- rowSums(mm) > 5
norm <- t(t(mm)/colSums(mm)) * gm(colSums(mm))
delta <- optimize(myFun, interval = c(1e-04, 0.99),
tol = 1e-06, maximum = TRUE, y = norm[rs5, ],
der = 0, doSum = FALSE)
dd[i, j] = sqrt(delta$maximum/(1 - delta$maximum))
}
}
--
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