[BioC] qspline Normalization

[Paul Boutros]

Hi all,

I'd like to use the qspline normalization method:
normalize.celfile.qspline {affy}

I have two problems with this:
a) I would like to use this normalization on cDNA data.  Am I correct in
interpreting that this method can either be fun directly on a
Cel.container object, or alternately can be called a data.matrix of
intensity values and a target vector?  Or do I need to do something in
addition to use it for non-Affy data?

b) I am a bit unclear on some of the arguments, and I am unsure how to
pick appropriate levels.  In particular, I am unclear about how to
determine realistic values for:
fit.iters
spline.method
spar
incl.ends
na.rm

Any advice or ideas would be very much appreciated.  And if this isn't the
right place for these questions, guidance on where to go would also be
welcome.

Paul