[BioC] normalize.invariantset usage

[Ben Bolstad]

Not a direct answer to your question, but if you use the affyPLM package
you can normalize exprSets. See for example

normalize.exprSet.quantiles
normalize.exprSet.qspline
normalize.exprSet.invariantset
.....


and directly using normalize()

eg

normalize(eset,method="quantiles")

Thanks,

Ben




On Mon, 2004-01-05 at 12:13, david neil hayes wrote:
> 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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-- 
Ben Bolstad <bolstad at stat.berkeley.edu>
http://www.stat.berkeley.edu/~bolstad