[BioC] normalize.invariantset usage

[david neil hayes]

I am interested in normalizing an expression matrix (not an affybatch) using 
the function "normalize.invariantset".  I have had luck with the related 
normalization functions: normalize.constant,  normalize.loess, 
normalize.quantiles (to name a few).

Normalize.invariantset, unlike the other functions mentioned, does not 
accept as its input a matrix of expression values, but rather a vector of 
expression values (presumably from one chip), as well as a vector of 
expression values against which to normalize (presumably a second chip?).  
The function returns a list of length 2 comprised of 1 object of class 
"smooth.spline" and 1 object which is a logical vector of the genes 
comprising the invariant set.

What I don't understand is how to obtain the normalized expression values 
for all gene in the vector from the smooth.spline object (The smooth.spline 
only seems to contain normalized expression for the invariant set).  I 
suspect it is simple, but I have been unable to figure this out.

Thanks in advance.
Neil Hayes

using R1.8.1 on the Windows XP, package=affy1.3.26

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