[BioC] edgeR plotMDS.DGEList() use of normalized counts

[Ted Toal [guest]]

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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