[BioC] Bug in normalizeBetweenArrays, method="Rquantile"

[Marcus Davy]

Gordon,
the M values for the Rquantile normalization are incorrect, the code is currently calculating M as

M = M - E
    = (R - G ) - (qR - R)                   - qR is quantile normalized R channel, R and G are log channel intensities
    = 2R -G -qR

Quick fix is to change the sign on line 61 of the code chunk :

 Rquantile = {
        R <- object$A + object$M/2
        E <- normalizeQuantiles(R, ...) - R
        object$M <- object$M - E                     # wrong sign
        object$A <- object$A + E/2
    }

to 

  Rquantile = {
        R <- object$A + object$M/2
        E <- normalizeQuantiles(R, ...) - R
        object$M <- object$M + E                    # sign change
        object$A <- object$A + E/2
    }

then M = qR - G, A = (qR+G)/2.

> packageDescription("limma", field="Version")
[1] "1.8.12"

marcus



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