[BioC] normalizeWithArray with method of "control" in limma package

[Leon Yee]

Hi all,

    I am very doubtful about the "control" method of 
normalizeWithinArray function in limma package.
    Suppose that I have an MAList object ma contains a two-color array:

w = rep(1, dim(ma$M)[1])
w[ abs(ma$M) > 3]  = 0

What is the difference between
normalizeWithinArray(ma, method="control", layout=layout,
    controlspots= as.logical(abs(1-w)) )

and

normalizeWithinArray(ma, method="loess", weights=w)

?

In practice, the first one with method="control" is very very slow,
while the second one is very quick.

The motivation of my trying these methods is that I want to do loess
normalization with only those probes that were not heavily
differential-expressed.

Could you help me out? Thanks in advance.


Leon