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Last seen 10.5 years ago
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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