[BioC] normalizeWithArray with method of "control" in limma package
Gordon K Smyth
smyth at wehi.EDU.AU
Tue Jan 6 01:33:57 CET 2009
method="control" does what you want exactly whereas weights=w is an
approximation. The exact method takes longer. See
Weights=w is an approximation because the loess curve setup uses all the
points to define the neighbourhood regions, even those for which w=0, and
so the loess curve definition is not the same as would you like to define
for the control spots alone.
method="control" is slow because it is necessary to store the loess fit
and then to compute predicted values for the non-control spots.
> Date: Sun, 04 Jan 2009 19:11:17 +0800
> From: Leon Yee <yee.leon at gmail.com>
> Subject: [BioC] normalizeWithArray with method of "control" in limma
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <49609955.9080502 at gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 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$M))
> w[ abs(ma$M) > 3] = 0
> What is the difference between
> normalizeWithinArray(ma, method="control", layout=layout,
> controlspots= as.logical(abs(1-w)) )
> 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
> Could you help me out? Thanks in advance.
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